Starting phenix.real_space_refine on Sat May 17 03:05:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swx_40824/05_2025/8swx_40824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swx_40824/05_2025/8swx_40824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8swx_40824/05_2025/8swx_40824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swx_40824/05_2025/8swx_40824.map" model { file = "/net/cci-nas-00/data/ceres_data/8swx_40824/05_2025/8swx_40824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swx_40824/05_2025/8swx_40824.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9452 2.51 5 N 2592 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15170 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3422 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 4 Chain: "B" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 950 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3433 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 4 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 950 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "F" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3441 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain breaks: 4 Chain: "H" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 465 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 92} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 93} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "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: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 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: "F" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 9.41, per 1000 atoms: 0.62 Number of scatterers: 15170 At special positions: 0 Unit cell: (134.03, 123.72, 148.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3024 8.00 N 2592 7.00 C 9452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.08 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.12 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 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 332 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 445 " distance=2.10 Simple disulfide: pdb=" SG CYS E 386 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.05 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.07 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.05 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 332 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 386 " - pdb=" SG CYS F 418 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 241 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 355 " " NAG A 611 " - " ASN A 363 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 448 " " NAG A 614 " - " ASN A 295 " " NAG A 615 " - " ASN A 289 " " NAG A 616 " - " ASN A 339 " " NAG A 617 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 241 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 333 " " NAG E 609 " - " ASN E 340 " " NAG E 610 " - " ASN E 364 " " NAG E 611 " - " ASN E 448 " " NAG E 612 " - " ASN E 133 " " NAG E 613 " - " ASN E 295 " " NAG E 614 " - " ASN E 356 " " NAG E 615 " - " ASN E 387 " " NAG E 616 " - " ASN E 393 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 241 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 289 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 333 " " NAG F 612 " - " ASN F 340 " " NAG F 613 " - " ASN F 387 " " NAG F 614 " - " ASN F 448 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN E 156 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN F 262 " Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 3526 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 27 sheets defined 26.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.013A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.893A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 481 through 484 removed outlier: 4.755A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.427A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 572 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 663 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 572 through 596 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 639 through 661 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.144A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 336 through 349 Processing helix chain 'E' and resid 350 through 354 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.878A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 547 removed outlier: 3.504A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 67 through 73 Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.221A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 336 through 351 Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.133A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.769A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.190A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.363A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.544A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, 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 284 through 302 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 414 through 417 current: chain 'A' and resid 468 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.544A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 373 through 374 Processing sheet with id=AB1, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.161A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.152A pdb=" N ASN E 241 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL E 89 " --> pdb=" O ASN E 241 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N SER E 243 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N GLU E 87 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N VAL E 245 " --> pdb=" O HIS E 85 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N HIS E 85 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.684A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB6, 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 309 removed outlier: 6.515A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (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 382 through 386 removed outlier: 4.296A pdb=" N PHE E 383 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 413 through 421 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB7, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.208A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.587A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 302 removed outlier: 7.358A pdb=" N GLN F 293 " --> pdb=" O SER F 335 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER F 335 " --> pdb=" O GLN F 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 330 through 335 current: chain 'F' and resid 382 through 386 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 386 current: chain 'F' and resid 466 through 470 Processing sheet with id=AC5, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.523A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AC7, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AC8, first strand: chain 'L' and resid 39 through 44 removed outlier: 6.859A pdb=" N UNK L 29 " --> pdb=" O UNK L 41 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N UNK L 43 " --> pdb=" O UNK L 27 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 56 through 61 removed outlier: 5.751A pdb=" N UNK L 57 " --> pdb=" O UNK L 68 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1284 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: 4.96 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3196 1.32 - 1.46: 4745 1.46 - 1.59: 7287 1.59 - 1.73: 71 1.73 - 1.87: 130 Bond restraints: 15429 Sorted by residual: bond pdb=" CB HIS E 375 " pdb=" CG HIS E 375 " ideal model delta sigma weight residual 1.497 1.372 0.125 1.40e-02 5.10e+03 7.94e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.57e+01 bond pdb=" CD2 TRP B 571 " pdb=" CE3 TRP B 571 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.29e+01 bond pdb=" CZ2 TRP C 571 " pdb=" CH2 TRP C 571 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.12e+01 bond pdb=" CZ2 TRP B 571 " pdb=" CH2 TRP B 571 " ideal model delta sigma weight residual 1.368 1.488 -0.120 1.90e-02 2.77e+03 4.00e+01 ... (remaining 15424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 18771 2.68 - 5.36: 1979 5.36 - 8.04: 211 8.04 - 10.72: 14 10.72 - 13.40: 2 Bond angle restraints: 20977 Sorted by residual: angle pdb=" C PHE F 233 " pdb=" N ASN F 234 " pdb=" CA ASN F 234 " ideal model delta sigma weight residual 120.28 133.68 -13.40 1.34e+00 5.57e-01 1.00e+02 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.76 -8.20 1.01e+00 9.80e-01 6.59e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.87 128.27 -8.40 1.04e+00 9.25e-01 6.53e+01 angle pdb=" N GLU A 87 " pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 111.36 119.87 -8.51 1.09e+00 8.42e-01 6.09e+01 angle pdb=" N CYS E 196 " pdb=" CA CYS E 196 " pdb=" C CYS E 196 " ideal model delta sigma weight residual 113.43 103.62 9.81 1.26e+00 6.30e-01 6.06e+01 ... (remaining 20972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 9899 21.13 - 42.25: 209 42.25 - 63.38: 64 63.38 - 84.51: 23 84.51 - 105.64: 14 Dihedral angle restraints: 10209 sinusoidal: 4798 harmonic: 5411 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual 93.00 151.82 -58.82 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.24 40.24 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.88 39.88 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 10206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1716 0.099 - 0.198: 556 0.198 - 0.297: 168 0.297 - 0.396: 108 0.396 - 0.495: 66 Chirality restraints: 2614 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.38e+02 ... (remaining 2611 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " 0.082 2.00e-02 2.50e+03 8.87e-02 9.84e+01 pdb=" CG ASN A 392 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " -0.140 2.00e-02 2.50e+03 pdb=" C1 NAG A 617 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 160 " 0.082 2.00e-02 2.50e+03 8.65e-02 9.36e+01 pdb=" CG ASN F 160 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN F 160 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN F 160 " -0.134 2.00e-02 2.50e+03 pdb=" C1 NAG F 602 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 393 " -0.068 2.00e-02 2.50e+03 7.09e-02 6.29e+01 pdb=" CG ASN E 393 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 393 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 393 " 0.110 2.00e-02 2.50e+03 pdb=" C1 NAG E 616 " -0.086 2.00e-02 2.50e+03 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3524 2.80 - 3.32: 13801 3.32 - 3.85: 24160 3.85 - 4.37: 29274 4.37 - 4.90: 46462 Nonbonded interactions: 117221 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.272 3.040 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.391 3.120 nonbonded pdb=" OD2 ASP C 632 " pdb=" NZ LYS E 46 " model vdw 2.399 3.120 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.407 2.496 nonbonded pdb=" OE2 GLU E 83 " pdb=" NZ LYS E 227 " model vdw 2.418 3.120 ... (remaining 117216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 66 through 395 or resid 412 through \ 504 or resid 601 through 614)) selection = (chain 'E' and (resid 33 through 182 or resid 189 through 396 or resid 412 throu \ gh 457 or resid 465 through 504 or resid 601 through 614)) selection = (chain 'F' and (resid 33 through 182 or resid 189 through 396 or resid 412 throu \ gh 464 or resid 466 through 504 or resid 601 through 614)) } ncs_group { reference = (chain 'B' and (resid 522 through 663 or resid 702 through 703)) selection = chain 'C' selection = (chain 'D' and (resid 522 through 663 or resid 702 through 703)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.590 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.125 15532 Z= 1.179 Angle : 1.721 13.400 21253 Z= 1.100 Chirality : 0.141 0.495 2614 Planarity : 0.009 0.049 2601 Dihedral : 11.067 105.636 6584 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.35 % Favored : 97.52 % Rotamer: Outliers : 0.41 % Allowed : 0.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1616 helix: 0.62 (0.25), residues: 376 sheet: 0.88 (0.24), residues: 414 loop : 0.45 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.009 TRP E 35 HIS 0.008 0.002 HIS F 216 PHE 0.030 0.006 PHE E 354 TYR 0.042 0.007 TYR F 191 ARG 0.008 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.08298 ( 61) link_NAG-ASN : angle 2.72330 ( 183) link_BETA1-4 : bond 0.07537 ( 9) link_BETA1-4 : angle 5.20850 ( 27) hydrogen bonds : bond 0.15852 ( 475) hydrogen bonds : angle 7.40783 ( 1284) SS BOND : bond 0.02373 ( 33) SS BOND : angle 3.02553 ( 66) covalent geometry : bond 0.02179 (15429) covalent geometry : angle 1.69436 (20977) *********************** 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 624 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 618 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9166 (m100) cc_final: 0.8844 (m100) REVERT: A 69 TRP cc_start: 0.8686 (m-90) cc_final: 0.8162 (m-90) REVERT: A 97 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8647 (tptt) REVERT: A 256 SER cc_start: 0.9586 (p) cc_final: 0.9165 (t) REVERT: A 257 THR cc_start: 0.8826 (p) cc_final: 0.8435 (t) REVERT: A 278 THR cc_start: 0.8503 (p) cc_final: 0.8012 (t) REVERT: A 377 ASN cc_start: 0.7972 (t0) cc_final: 0.7680 (t0) REVERT: A 474 ASP cc_start: 0.8139 (t70) cc_final: 0.7654 (p0) REVERT: B 576 LEU cc_start: 0.9123 (tp) cc_final: 0.8919 (tp) REVERT: B 618 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7264 (m-40) REVERT: B 650 GLN cc_start: 0.9134 (tp40) cc_final: 0.8831 (tp40) REVERT: B 653 GLN cc_start: 0.7819 (mt0) cc_final: 0.7480 (mt0) REVERT: C 530 MET cc_start: 0.8150 (mtm) cc_final: 0.7794 (mtp) REVERT: C 575 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8193 (tp40) REVERT: C 601 LYS cc_start: 0.8824 (mttp) cc_final: 0.8534 (mtpp) REVERT: C 605 CYS cc_start: 0.6791 (m) cc_final: 0.6343 (m) REVERT: E 33 ASN cc_start: 0.7243 (m-40) cc_final: 0.6608 (t0) REVERT: E 35 TRP cc_start: 0.8574 (m100) cc_final: 0.8286 (m100) REVERT: E 106 THR cc_start: 0.9200 (m) cc_final: 0.8474 (m) REVERT: E 306 SER cc_start: 0.8834 (m) cc_final: 0.8474 (p) REVERT: E 490 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8790 (ttpp) REVERT: E 491 ILE cc_start: 0.9137 (mm) cc_final: 0.8810 (tp) REVERT: E 498 PRO cc_start: 0.9040 (Cg_endo) cc_final: 0.8833 (Cg_exo) REVERT: D 530 MET cc_start: 0.8448 (mtp) cc_final: 0.8067 (mtp) REVERT: F 111 LEU cc_start: 0.8617 (tp) cc_final: 0.8245 (tp) REVERT: F 183 GLN cc_start: 0.7899 (tt0) cc_final: 0.7589 (tt0) REVERT: F 426 MET cc_start: 0.7943 (mtp) cc_final: 0.7208 (mmp) REVERT: F 478 ASN cc_start: 0.8873 (m-40) cc_final: 0.8250 (t0) REVERT: F 494 LEU cc_start: 0.9228 (tp) cc_final: 0.8887 (tp) REVERT: F 500 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6427 (mtm-85) outliers start: 6 outliers final: 5 residues processed: 624 average time/residue: 0.2734 time to fit residues: 246.7317 Evaluate side-chains 384 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 378 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 160 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 279 ASN A 425 ASN B 540 GLN B 616 ASN B 640 GLN B 656 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN D 543 ASN D 656 ASN F 72 HIS F 133 ASN F 170 GLN F 203 GLN F 432 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.152599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129195 restraints weight = 22967.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132970 restraints weight = 12642.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135509 restraints weight = 8370.211| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15532 Z= 0.177 Angle : 0.795 10.200 21253 Z= 0.388 Chirality : 0.050 0.384 2614 Planarity : 0.004 0.052 2601 Dihedral : 8.103 73.181 3440 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 3.72 % Allowed : 13.73 % Favored : 82.56 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1616 helix: 1.80 (0.27), residues: 381 sheet: 0.86 (0.24), residues: 434 loop : -0.02 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 479 HIS 0.005 0.001 HIS A 374 PHE 0.025 0.003 PHE F 468 TYR 0.022 0.002 TYR F 173 ARG 0.011 0.001 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 61) link_NAG-ASN : angle 3.09841 ( 183) link_BETA1-4 : bond 0.01019 ( 9) link_BETA1-4 : angle 3.78750 ( 27) hydrogen bonds : bond 0.06179 ( 475) hydrogen bonds : angle 5.83068 ( 1284) SS BOND : bond 0.00346 ( 33) SS BOND : angle 1.28204 ( 66) covalent geometry : bond 0.00386 (15429) covalent geometry : angle 0.72980 (20977) *********************** 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 483 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 428 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8637 (m-90) cc_final: 0.8392 (m-90) REVERT: A 87 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 97 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8556 (tptp) REVERT: A 256 SER cc_start: 0.9514 (p) cc_final: 0.9185 (t) REVERT: A 278 THR cc_start: 0.8748 (p) cc_final: 0.8323 (t) REVERT: A 356 ASN cc_start: 0.8780 (p0) cc_final: 0.8575 (p0) REVERT: A 466 GLU cc_start: 0.6430 (pp20) cc_final: 0.5769 (mm-30) REVERT: A 474 ASP cc_start: 0.8174 (t70) cc_final: 0.7796 (p0) REVERT: B 618 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.7032 (m-40) REVERT: B 621 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7233 (mt-10) REVERT: B 626 MET cc_start: 0.7955 (ttt) cc_final: 0.7536 (ttm) REVERT: B 652 GLN cc_start: 0.7285 (tm-30) cc_final: 0.6848 (tm-30) REVERT: C 601 LYS cc_start: 0.8837 (mttp) cc_final: 0.8413 (mtpp) REVERT: C 645 LEU cc_start: 0.9215 (mt) cc_final: 0.8901 (mt) REVERT: E 35 TRP cc_start: 0.8598 (m100) cc_final: 0.8188 (m100) REVERT: E 102 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6800 (tm-30) REVERT: E 178 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7597 (ttp80) REVERT: E 209 SER cc_start: 0.8965 (t) cc_final: 0.8750 (p) REVERT: E 273 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8202 (mtt180) REVERT: E 306 SER cc_start: 0.8765 (m) cc_final: 0.8245 (p) REVERT: E 498 PRO cc_start: 0.9021 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: D 530 MET cc_start: 0.8663 (mtp) cc_final: 0.8317 (mtp) REVERT: F 39 TYR cc_start: 0.9037 (m-80) cc_final: 0.8832 (m-80) REVERT: F 178 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7665 (ttm110) REVERT: F 426 MET cc_start: 0.7440 (mtp) cc_final: 0.6962 (mmp) REVERT: F 500 ARG cc_start: 0.6642 (mtt180) cc_final: 0.6203 (mtm-85) outliers start: 55 outliers final: 31 residues processed: 463 average time/residue: 0.2467 time to fit residues: 169.8283 Evaluate side-chains 396 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 182 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 616 ASN B 640 GLN E 105 HIS E 195 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN F 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.123670 restraints weight = 23715.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.127211 restraints weight = 13346.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129592 restraints weight = 9011.564| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15532 Z= 0.212 Angle : 0.758 13.627 21253 Z= 0.365 Chirality : 0.050 0.350 2614 Planarity : 0.004 0.054 2601 Dihedral : 7.080 59.067 3440 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 5.14 % Allowed : 15.35 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1616 helix: 1.47 (0.27), residues: 388 sheet: 0.70 (0.24), residues: 423 loop : -0.28 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 479 HIS 0.007 0.001 HIS E 375 PHE 0.018 0.002 PHE E 354 TYR 0.019 0.002 TYR E 484 ARG 0.008 0.001 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 61) link_NAG-ASN : angle 3.01509 ( 183) link_BETA1-4 : bond 0.00597 ( 9) link_BETA1-4 : angle 3.03750 ( 27) hydrogen bonds : bond 0.05189 ( 475) hydrogen bonds : angle 5.41471 ( 1284) SS BOND : bond 0.00406 ( 33) SS BOND : angle 1.31872 ( 66) covalent geometry : bond 0.00488 (15429) covalent geometry : angle 0.69647 (20977) *********************** 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 464 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 388 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8902 (ttm) cc_final: 0.8455 (tpp) REVERT: A 176 PHE cc_start: 0.8648 (m-80) cc_final: 0.8445 (m-80) REVERT: A 177 TYR cc_start: 0.9262 (m-80) cc_final: 0.8761 (m-80) REVERT: A 192 ARG cc_start: 0.6733 (mpt-90) cc_final: 0.6029 (mpp80) REVERT: A 197 ASN cc_start: 0.7145 (p0) cc_final: 0.6704 (m110) REVERT: A 278 THR cc_start: 0.8960 (p) cc_final: 0.8497 (t) REVERT: A 422 GLN cc_start: 0.8171 (mt0) cc_final: 0.7885 (mt0) REVERT: A 474 ASP cc_start: 0.8375 (t70) cc_final: 0.7799 (p0) REVERT: A 484 TYR cc_start: 0.8948 (p90) cc_final: 0.8715 (p90) REVERT: B 626 MET cc_start: 0.7997 (ttt) cc_final: 0.7621 (ttm) REVERT: C 601 LYS cc_start: 0.8896 (mttp) cc_final: 0.8516 (mtpp) REVERT: E 35 TRP cc_start: 0.8663 (m100) cc_final: 0.8221 (m100) REVERT: E 102 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6922 (tm-30) REVERT: E 103 GLN cc_start: 0.9098 (tp40) cc_final: 0.8132 (tm-30) REVERT: E 121 LYS cc_start: 0.8225 (mmtt) cc_final: 0.8012 (tptt) REVERT: E 178 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7602 (tmm160) REVERT: E 273 ARG cc_start: 0.8687 (mtt90) cc_final: 0.8420 (mtt180) REVERT: E 306 SER cc_start: 0.8871 (m) cc_final: 0.8592 (p) REVERT: E 456 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7388 (ttp80) REVERT: F 97 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8419 (mmmm) REVERT: F 136 ASN cc_start: 0.7703 (t0) cc_final: 0.7433 (t0) REVERT: F 178 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7661 (ttm110) REVERT: F 379 CYS cc_start: 0.7761 (t) cc_final: 0.7548 (t) REVERT: F 426 MET cc_start: 0.7601 (mtp) cc_final: 0.7104 (mmp) outliers start: 76 outliers final: 50 residues processed: 429 average time/residue: 0.2566 time to fit residues: 163.8100 Evaluate side-chains 388 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 274 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN D 607 ASN D 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.148134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.125067 restraints weight = 23636.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128684 restraints weight = 13114.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.131056 restraints weight = 8735.625| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15532 Z= 0.135 Angle : 0.683 19.873 21253 Z= 0.322 Chirality : 0.047 0.365 2614 Planarity : 0.004 0.057 2601 Dihedral : 6.156 59.278 3436 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 4.33 % Allowed : 17.44 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1616 helix: 1.97 (0.28), residues: 371 sheet: 0.71 (0.24), residues: 443 loop : -0.34 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.005 0.001 HIS A 374 PHE 0.016 0.002 PHE B 522 TYR 0.013 0.001 TYR A 173 ARG 0.008 0.000 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 61) link_NAG-ASN : angle 3.38423 ( 183) link_BETA1-4 : bond 0.00506 ( 9) link_BETA1-4 : angle 2.42335 ( 27) hydrogen bonds : bond 0.04479 ( 475) hydrogen bonds : angle 5.02980 ( 1284) SS BOND : bond 0.00302 ( 33) SS BOND : angle 0.94936 ( 66) covalent geometry : bond 0.00298 (15429) covalent geometry : angle 0.60150 (20977) *********************** 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 443 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 379 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.9246 (m-80) cc_final: 0.8962 (m-80) REVERT: A 192 ARG cc_start: 0.6735 (mpt-90) cc_final: 0.6015 (mpp80) REVERT: A 195 ASN cc_start: 0.8185 (m110) cc_final: 0.7903 (t0) REVERT: A 278 THR cc_start: 0.8909 (p) cc_final: 0.8380 (t) REVERT: A 474 ASP cc_start: 0.8359 (t70) cc_final: 0.7938 (p0) REVERT: A 482 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8002 (mt-10) REVERT: A 484 TYR cc_start: 0.8896 (p90) cc_final: 0.8588 (p90) REVERT: A 486 TYR cc_start: 0.8643 (m-80) cc_final: 0.8416 (m-80) REVERT: B 626 MET cc_start: 0.7971 (ttt) cc_final: 0.7604 (ttm) REVERT: C 601 LYS cc_start: 0.8881 (mttp) cc_final: 0.8615 (mtpt) REVERT: E 35 TRP cc_start: 0.8672 (m100) cc_final: 0.8231 (m100) REVERT: E 102 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7069 (tm-30) REVERT: E 103 GLN cc_start: 0.9112 (tp40) cc_final: 0.8316 (tm-30) REVERT: E 177 TYR cc_start: 0.8247 (m-80) cc_final: 0.7783 (m-80) REVERT: E 178 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7622 (tmm160) REVERT: E 273 ARG cc_start: 0.8583 (mtt90) cc_final: 0.8362 (mtt180) REVERT: E 469 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7447 (ptp-110) REVERT: F 97 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8382 (mmmm) REVERT: F 136 ASN cc_start: 0.7684 (t0) cc_final: 0.7447 (t0) REVERT: F 153 GLU cc_start: 0.6461 (tp30) cc_final: 0.5752 (tp30) REVERT: F 178 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7597 (ttm110) REVERT: F 258 GLN cc_start: 0.9039 (mt0) cc_final: 0.8428 (mt0) REVERT: F 426 MET cc_start: 0.7679 (mtp) cc_final: 0.7205 (mmp) REVERT: F 432 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8103 (mm-40) outliers start: 64 outliers final: 51 residues processed: 405 average time/residue: 0.2490 time to fit residues: 148.4683 Evaluate side-chains 399 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 347 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 432 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 145 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 630 GLN D 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.122766 restraints weight = 24236.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126260 restraints weight = 13477.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.128618 restraints weight = 9042.416| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15532 Z= 0.178 Angle : 0.704 20.388 21253 Z= 0.335 Chirality : 0.048 0.366 2614 Planarity : 0.004 0.059 2601 Dihedral : 6.044 59.059 3436 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Rotamer: Outliers : 5.68 % Allowed : 17.11 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1616 helix: 1.84 (0.28), residues: 369 sheet: 0.56 (0.25), residues: 432 loop : -0.46 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 339 HIS 0.005 0.001 HIS E 375 PHE 0.013 0.002 PHE B 522 TYR 0.019 0.002 TYR F 173 ARG 0.007 0.001 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 61) link_NAG-ASN : angle 3.30971 ( 183) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 2.30160 ( 27) hydrogen bonds : bond 0.04572 ( 475) hydrogen bonds : angle 5.00294 ( 1284) SS BOND : bond 0.00353 ( 33) SS BOND : angle 1.35685 ( 66) covalent geometry : bond 0.00412 (15429) covalent geometry : angle 0.62780 (20977) *********************** 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 443 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 359 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8838 (ttm) cc_final: 0.8615 (tpp) REVERT: A 177 TYR cc_start: 0.9276 (m-80) cc_final: 0.9057 (m-80) REVERT: A 190 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6421 (tm-30) REVERT: A 192 ARG cc_start: 0.6757 (mpt-90) cc_final: 0.6314 (mpt-90) REVERT: A 278 THR cc_start: 0.8953 (p) cc_final: 0.8453 (t) REVERT: A 414 ILE cc_start: 0.8495 (mt) cc_final: 0.8123 (tt) REVERT: A 474 ASP cc_start: 0.8521 (t70) cc_final: 0.7933 (p0) REVERT: A 475 MET cc_start: 0.8620 (mmm) cc_final: 0.8343 (mmm) REVERT: A 482 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 484 TYR cc_start: 0.8886 (p90) cc_final: 0.8651 (p90) REVERT: A 486 TYR cc_start: 0.8732 (m-80) cc_final: 0.8369 (m-80) REVERT: B 626 MET cc_start: 0.7995 (ttt) cc_final: 0.7644 (ttm) REVERT: C 601 LYS cc_start: 0.8883 (mttp) cc_final: 0.8662 (mtpt) REVERT: E 35 TRP cc_start: 0.8754 (m100) cc_final: 0.8277 (m100) REVERT: E 103 GLN cc_start: 0.9161 (tp40) cc_final: 0.8392 (tm-30) REVERT: E 273 ARG cc_start: 0.8572 (mtt90) cc_final: 0.8184 (mtt180) REVERT: E 469 ARG cc_start: 0.8209 (mtt-85) cc_final: 0.7464 (ptp-110) REVERT: F 82 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: F 97 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8397 (mmmm) REVERT: F 136 ASN cc_start: 0.7764 (t0) cc_final: 0.7516 (t0) REVERT: F 178 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7600 (ttm110) REVERT: F 258 GLN cc_start: 0.9038 (mt0) cc_final: 0.8427 (mt0) REVERT: F 280 ASN cc_start: 0.8997 (p0) cc_final: 0.8792 (p0) REVERT: F 426 MET cc_start: 0.7716 (mtp) cc_final: 0.7331 (mmp) REVERT: F 432 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8139 (mm-40) outliers start: 84 outliers final: 64 residues processed: 401 average time/residue: 0.2635 time to fit residues: 156.6874 Evaluate side-chains 408 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 432 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 160 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 143 optimal weight: 0.5980 chunk 177 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 575 GLN C 630 GLN D 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.147706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.125009 restraints weight = 23863.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128551 restraints weight = 13213.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130894 restraints weight = 8819.963| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15532 Z= 0.127 Angle : 0.681 20.081 21253 Z= 0.318 Chirality : 0.047 0.361 2614 Planarity : 0.004 0.059 2601 Dihedral : 6.019 59.840 3436 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 4.53 % Allowed : 18.86 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1616 helix: 1.81 (0.28), residues: 375 sheet: 0.56 (0.25), residues: 432 loop : -0.50 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 339 HIS 0.004 0.001 HIS A 374 PHE 0.034 0.002 PHE A 391 TYR 0.014 0.001 TYR F 173 ARG 0.010 0.000 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 61) link_NAG-ASN : angle 3.52629 ( 183) link_BETA1-4 : bond 0.00435 ( 9) link_BETA1-4 : angle 1.93037 ( 27) hydrogen bonds : bond 0.04266 ( 475) hydrogen bonds : angle 4.84659 ( 1284) SS BOND : bond 0.00263 ( 33) SS BOND : angle 1.31832 ( 66) covalent geometry : bond 0.00286 (15429) covalent geometry : angle 0.59238 (20977) *********************** 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 437 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 370 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8791 (ttm) cc_final: 0.8572 (tpp) REVERT: A 177 TYR cc_start: 0.9234 (m-80) cc_final: 0.9021 (m-80) REVERT: A 190 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6675 (tm-30) REVERT: A 192 ARG cc_start: 0.6711 (mpt-90) cc_final: 0.6284 (mpt-90) REVERT: A 195 ASN cc_start: 0.8244 (m110) cc_final: 0.7263 (t0) REVERT: A 278 THR cc_start: 0.8912 (p) cc_final: 0.8371 (t) REVERT: A 414 ILE cc_start: 0.8586 (mt) cc_final: 0.8224 (tt) REVERT: A 474 ASP cc_start: 0.8526 (t70) cc_final: 0.7953 (p0) REVERT: A 475 MET cc_start: 0.8558 (mmm) cc_final: 0.8315 (mmm) REVERT: A 482 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 486 TYR cc_start: 0.8702 (m-80) cc_final: 0.8394 (m-80) REVERT: B 626 MET cc_start: 0.7973 (ttt) cc_final: 0.7626 (ttm) REVERT: E 35 TRP cc_start: 0.8739 (m100) cc_final: 0.8284 (m100) REVERT: E 103 GLN cc_start: 0.9148 (tp40) cc_final: 0.8400 (tm-30) REVERT: E 177 TYR cc_start: 0.8253 (m-80) cc_final: 0.7829 (m-80) REVERT: E 178 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.7742 (tmm160) REVERT: E 469 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7493 (ptp-110) REVERT: F 82 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: F 136 ASN cc_start: 0.7775 (t0) cc_final: 0.7511 (t0) REVERT: F 258 GLN cc_start: 0.8989 (mt0) cc_final: 0.8388 (mt0) REVERT: F 426 MET cc_start: 0.7751 (mtp) cc_final: 0.7390 (mmp) outliers start: 67 outliers final: 55 residues processed: 405 average time/residue: 0.2491 time to fit residues: 151.4799 Evaluate side-chains 408 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 352 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 374 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 179 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 216 HIS B 616 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.140937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.117639 restraints weight = 24614.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121088 restraints weight = 13798.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123416 restraints weight = 9326.278| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 15532 Z= 0.288 Angle : 0.830 23.372 21253 Z= 0.391 Chirality : 0.053 0.664 2614 Planarity : 0.005 0.062 2601 Dihedral : 6.824 58.307 3436 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.08 % Favored : 95.85 % Rotamer: Outliers : 5.21 % Allowed : 18.66 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1616 helix: 1.19 (0.27), residues: 381 sheet: 0.12 (0.25), residues: 418 loop : -0.72 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 45 HIS 0.007 0.001 HIS E 375 PHE 0.026 0.003 PHE A 391 TYR 0.018 0.002 TYR A 191 ARG 0.013 0.001 ARG C 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 61) link_NAG-ASN : angle 3.87671 ( 183) link_BETA1-4 : bond 0.00354 ( 9) link_BETA1-4 : angle 2.42212 ( 27) hydrogen bonds : bond 0.05156 ( 475) hydrogen bonds : angle 5.29116 ( 1284) SS BOND : bond 0.00516 ( 33) SS BOND : angle 1.38021 ( 66) covalent geometry : bond 0.00674 (15429) covalent geometry : angle 0.74424 (20977) *********************** 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 444 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 367 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9079 (mptt) cc_final: 0.8374 (tptp) REVERT: A 177 TYR cc_start: 0.9297 (m-80) cc_final: 0.9049 (m-80) REVERT: A 190 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6321 (tm-30) REVERT: A 192 ARG cc_start: 0.6510 (mpt-90) cc_final: 0.5831 (mpt-90) REVERT: A 278 THR cc_start: 0.9073 (p) cc_final: 0.8548 (t) REVERT: A 325 ASP cc_start: 0.7982 (t0) cc_final: 0.7772 (t0) REVERT: A 414 ILE cc_start: 0.8574 (mt) cc_final: 0.8226 (tt) REVERT: A 474 ASP cc_start: 0.8595 (t70) cc_final: 0.7781 (p0) REVERT: A 482 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7996 (mt-10) REVERT: A 486 TYR cc_start: 0.8892 (m-80) cc_final: 0.8642 (m-80) REVERT: B 540 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8589 (mp-120) REVERT: B 621 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8004 (mp0) REVERT: B 624 ASP cc_start: 0.8721 (t70) cc_final: 0.8231 (t70) REVERT: E 35 TRP cc_start: 0.8847 (m100) cc_final: 0.7923 (m100) REVERT: E 121 LYS cc_start: 0.8476 (mptt) cc_final: 0.8027 (mmmm) REVERT: E 178 ARG cc_start: 0.8039 (ttp-170) cc_final: 0.7735 (tmm160) REVERT: F 82 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: F 426 MET cc_start: 0.7734 (mtp) cc_final: 0.6947 (mmt) REVERT: F 432 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8177 (mm-40) outliers start: 77 outliers final: 59 residues processed: 408 average time/residue: 0.2619 time to fit residues: 160.4077 Evaluate side-chains 404 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 342 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 432 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN C 630 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.146649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.123583 restraints weight = 23880.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127087 restraints weight = 13404.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129445 restraints weight = 9042.235| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15532 Z= 0.131 Angle : 0.721 19.813 21253 Z= 0.341 Chirality : 0.049 0.641 2614 Planarity : 0.004 0.059 2601 Dihedral : 6.376 58.603 3436 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.28 % Favored : 96.60 % Rotamer: Outliers : 3.92 % Allowed : 20.96 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1616 helix: 1.60 (0.28), residues: 374 sheet: 0.13 (0.24), residues: 441 loop : -0.71 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 339 HIS 0.003 0.001 HIS F 375 PHE 0.024 0.002 PHE A 391 TYR 0.013 0.001 TYR F 173 ARG 0.011 0.001 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 61) link_NAG-ASN : angle 3.43436 ( 183) link_BETA1-4 : bond 0.00432 ( 9) link_BETA1-4 : angle 1.68485 ( 27) hydrogen bonds : bond 0.04459 ( 475) hydrogen bonds : angle 4.92787 ( 1284) SS BOND : bond 0.00598 ( 33) SS BOND : angle 1.57368 ( 66) covalent geometry : bond 0.00294 (15429) covalent geometry : angle 0.64214 (20977) *********************** 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 422 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 364 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8800 (m-90) cc_final: 0.8598 (m-90) REVERT: A 97 LYS cc_start: 0.8980 (mptt) cc_final: 0.8220 (tptp) REVERT: A 190 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6696 (tm-30) REVERT: A 192 ARG cc_start: 0.6577 (mpt-90) cc_final: 0.6042 (mpt-90) REVERT: A 278 THR cc_start: 0.8910 (p) cc_final: 0.8367 (t) REVERT: A 414 ILE cc_start: 0.8565 (mt) cc_final: 0.8240 (tt) REVERT: A 474 ASP cc_start: 0.8584 (t70) cc_final: 0.7744 (p0) REVERT: A 475 MET cc_start: 0.8399 (mmm) cc_final: 0.8133 (mmm) REVERT: A 482 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7982 (mt-10) REVERT: A 486 TYR cc_start: 0.8709 (m-80) cc_final: 0.8463 (m-80) REVERT: B 626 MET cc_start: 0.7979 (ttt) cc_final: 0.7614 (ttm) REVERT: E 35 TRP cc_start: 0.8366 (m100) cc_final: 0.8049 (m100) REVERT: E 103 GLN cc_start: 0.9211 (tp40) cc_final: 0.8594 (tm-30) REVERT: E 177 TYR cc_start: 0.8227 (m-80) cc_final: 0.7857 (m-80) REVERT: E 178 ARG cc_start: 0.8057 (ttp-170) cc_final: 0.7797 (tmm160) REVERT: F 82 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: F 178 ARG cc_start: 0.7673 (ttm110) cc_final: 0.7335 (ttm110) REVERT: F 244 THR cc_start: 0.9000 (m) cc_final: 0.8745 (m) REVERT: F 258 GLN cc_start: 0.8862 (mt0) cc_final: 0.8631 (tt0) REVERT: F 426 MET cc_start: 0.7638 (mtp) cc_final: 0.7325 (mmp) REVERT: F 432 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8221 (mm-40) outliers start: 58 outliers final: 46 residues processed: 391 average time/residue: 0.2511 time to fit residues: 145.2607 Evaluate side-chains 391 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 343 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 432 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 82 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN B 630 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN E 425 ASN D 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122199 restraints weight = 23906.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125679 restraints weight = 13421.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.128000 restraints weight = 9040.195| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 15532 Z= 0.153 Angle : 0.715 19.560 21253 Z= 0.338 Chirality : 0.049 0.600 2614 Planarity : 0.004 0.061 2601 Dihedral : 6.275 59.045 3436 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.10 % Rotamer: Outliers : 3.99 % Allowed : 21.10 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1616 helix: 1.57 (0.27), residues: 375 sheet: 0.12 (0.24), residues: 425 loop : -0.73 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 339 HIS 0.005 0.001 HIS F 331 PHE 0.021 0.002 PHE A 391 TYR 0.015 0.001 TYR E 318 ARG 0.010 0.001 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 61) link_NAG-ASN : angle 3.37168 ( 183) link_BETA1-4 : bond 0.00423 ( 9) link_BETA1-4 : angle 1.76228 ( 27) hydrogen bonds : bond 0.04390 ( 475) hydrogen bonds : angle 4.85560 ( 1284) SS BOND : bond 0.00361 ( 33) SS BOND : angle 1.70961 ( 66) covalent geometry : bond 0.00357 (15429) covalent geometry : angle 0.63727 (20977) *********************** 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 407 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 348 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8744 (m-90) cc_final: 0.8528 (m-90) REVERT: A 97 LYS cc_start: 0.8969 (mptt) cc_final: 0.8220 (tptp) REVERT: A 177 TYR cc_start: 0.9194 (m-80) cc_final: 0.8895 (m-80) REVERT: A 190 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6442 (tm-30) REVERT: A 192 ARG cc_start: 0.6553 (mpt-90) cc_final: 0.5966 (mpt-90) REVERT: A 278 THR cc_start: 0.8889 (p) cc_final: 0.8344 (t) REVERT: A 414 ILE cc_start: 0.8583 (mt) cc_final: 0.8270 (tt) REVERT: A 422 GLN cc_start: 0.8186 (mt0) cc_final: 0.7830 (mt0) REVERT: A 474 ASP cc_start: 0.8594 (t70) cc_final: 0.7725 (p0) REVERT: A 482 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8041 (mt-10) REVERT: A 486 TYR cc_start: 0.8760 (m-80) cc_final: 0.8554 (m-80) REVERT: B 626 MET cc_start: 0.7990 (ttt) cc_final: 0.7657 (ttm) REVERT: E 35 TRP cc_start: 0.8468 (m100) cc_final: 0.8147 (m100) REVERT: E 103 GLN cc_start: 0.9213 (tp40) cc_final: 0.8669 (tm-30) REVERT: E 177 TYR cc_start: 0.8244 (m-80) cc_final: 0.7842 (m-80) REVERT: E 178 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7787 (tmm160) REVERT: E 457 ASP cc_start: 0.7641 (t0) cc_final: 0.7439 (t70) REVERT: F 82 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7595 (pm20) REVERT: F 178 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7355 (ttm110) REVERT: F 290 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8248 (mt-10) REVERT: F 426 MET cc_start: 0.7693 (mtp) cc_final: 0.7398 (mmt) REVERT: F 432 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8215 (mm-40) outliers start: 59 outliers final: 53 residues processed: 377 average time/residue: 0.2486 time to fit residues: 138.5579 Evaluate side-chains 390 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 432 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 107 optimal weight: 0.5980 chunk 160 optimal weight: 0.0270 chunk 72 optimal weight: 0.5980 chunk 138 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 173 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 616 ASN B 630 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.122191 restraints weight = 24141.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125700 restraints weight = 13471.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.128037 restraints weight = 9049.514| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 15532 Z= 0.196 Angle : 0.905 59.187 21253 Z= 0.482 Chirality : 0.050 0.597 2614 Planarity : 0.005 0.065 2601 Dihedral : 6.284 59.022 3434 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 3.99 % Allowed : 21.70 % Favored : 74.31 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1616 helix: 1.58 (0.27), residues: 375 sheet: 0.15 (0.24), residues: 424 loop : -0.72 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 339 HIS 0.004 0.001 HIS F 375 PHE 0.020 0.001 PHE A 391 TYR 0.069 0.002 TYR E 484 ARG 0.055 0.001 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00858 ( 61) link_NAG-ASN : angle 3.54758 ( 183) link_BETA1-4 : bond 0.00403 ( 9) link_BETA1-4 : angle 1.76422 ( 27) hydrogen bonds : bond 0.04376 ( 475) hydrogen bonds : angle 4.84806 ( 1284) SS BOND : bond 0.00376 ( 33) SS BOND : angle 1.69033 ( 66) covalent geometry : bond 0.00439 (15429) covalent geometry : angle 0.84107 (20977) ********************** 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 393 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 334 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8746 (m-90) cc_final: 0.8524 (m-90) REVERT: A 97 LYS cc_start: 0.8968 (mptt) cc_final: 0.8215 (tptp) REVERT: A 177 TYR cc_start: 0.9193 (m-80) cc_final: 0.8891 (m-80) REVERT: A 190 GLU cc_start: 0.6643 (tm-30) cc_final: 0.6382 (tm-30) REVERT: A 192 ARG cc_start: 0.6561 (mpt-90) cc_final: 0.5969 (mpt-90) REVERT: A 278 THR cc_start: 0.8898 (p) cc_final: 0.8338 (t) REVERT: A 414 ILE cc_start: 0.8581 (mt) cc_final: 0.8270 (tt) REVERT: A 422 GLN cc_start: 0.8202 (mt0) cc_final: 0.7817 (mt0) REVERT: A 474 ASP cc_start: 0.8592 (t70) cc_final: 0.7724 (p0) REVERT: A 482 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 486 TYR cc_start: 0.8758 (m-80) cc_final: 0.8552 (m-80) REVERT: B 626 MET cc_start: 0.8013 (ttt) cc_final: 0.7664 (ttm) REVERT: E 35 TRP cc_start: 0.8504 (m100) cc_final: 0.8210 (m100) REVERT: E 103 GLN cc_start: 0.9210 (tp40) cc_final: 0.8668 (tm-30) REVERT: E 177 TYR cc_start: 0.8242 (m-80) cc_final: 0.7833 (m-80) REVERT: E 178 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7781 (tmm160) REVERT: F 82 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: F 178 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7367 (ttm110) REVERT: F 290 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8243 (mt-10) REVERT: F 426 MET cc_start: 0.7672 (mtp) cc_final: 0.7353 (mmp) REVERT: F 432 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8213 (mm-40) outliers start: 59 outliers final: 53 residues processed: 360 average time/residue: 0.2480 time to fit residues: 133.7840 Evaluate side-chains 388 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 432 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 102 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 180 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN B 630 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122244 restraints weight = 24013.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125721 restraints weight = 13418.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.128066 restraints weight = 9028.966| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 15532 Z= 0.215 Angle : 0.913 59.187 21253 Z= 0.484 Chirality : 0.050 0.597 2614 Planarity : 0.005 0.065 2601 Dihedral : 6.284 59.022 3434 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 3.79 % Allowed : 21.77 % Favored : 74.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1616 helix: 1.58 (0.27), residues: 375 sheet: 0.15 (0.24), residues: 424 loop : -0.72 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 339 HIS 0.004 0.001 HIS F 375 PHE 0.020 0.001 PHE A 391 TYR 0.069 0.002 TYR E 484 ARG 0.055 0.001 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.03000 ( 61) link_NAG-ASN : angle 3.76564 ( 183) link_BETA1-4 : bond 0.00403 ( 9) link_BETA1-4 : angle 1.76422 ( 27) hydrogen bonds : bond 0.04376 ( 475) hydrogen bonds : angle 4.84806 ( 1284) SS BOND : bond 0.00376 ( 33) SS BOND : angle 1.69033 ( 66) covalent geometry : bond 0.00439 (15429) covalent geometry : angle 0.84108 (20977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4806.76 seconds wall clock time: 85 minutes 5.24 seconds (5105.24 seconds total)