Starting phenix.real_space_refine on Fri Jun 13 16:04:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swx_40824/06_2025/8swx_40824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swx_40824/06_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_40824/06_2025/8swx_40824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swx_40824/06_2025/8swx_40824.map" model { file = "/net/cci-nas-00/data/ceres_data/8swx_40824/06_2025/8swx_40824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swx_40824/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.04, per 1000 atoms: 0.60 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: 3.82 Conformation dependent library (CDL) restraints added in 1.4 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: 1.62 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: 4.42 Time building geometry restraints manager: 4.51 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: 0.010 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 33.450 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.040 ------------------------------------------------------------------------------- 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 : 1.562 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: 0.2883 time to fit residues: 261.3663 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 : 1.495 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.129211 restraints weight = 22967.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.132971 restraints weight = 12614.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135515 restraints weight = 8368.490| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- 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 : 1.456 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: 0.8639 (m-90) cc_final: 0.8393 (m-90) REVERT: A 87 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 97 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8554 (tptp) REVERT: A 256 SER cc_start: 0.9513 (p) cc_final: 0.9185 (t) REVERT: A 278 THR cc_start: 0.8750 (p) cc_final: 0.8325 (t) REVERT: A 356 ASN cc_start: 0.8783 (p0) cc_final: 0.8579 (p0) REVERT: A 466 GLU cc_start: 0.6432 (pp20) cc_final: 0.5768 (mm-30) REVERT: A 474 ASP cc_start: 0.8177 (t70) cc_final: 0.7795 (p0) REVERT: B 618 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.7033 (m-40) REVERT: B 621 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 626 MET cc_start: 0.7955 (ttt) cc_final: 0.7537 (ttm) REVERT: B 652 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6849 (tm-30) REVERT: C 601 LYS cc_start: 0.8837 (mttp) cc_final: 0.8413 (mtpp) REVERT: C 645 LEU cc_start: 0.9214 (mt) cc_final: 0.8899 (mt) REVERT: E 35 TRP cc_start: 0.8599 (m100) cc_final: 0.8188 (m100) REVERT: E 102 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6802 (tm-30) REVERT: E 178 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7601 (ttp80) REVERT: E 209 SER cc_start: 0.8964 (t) cc_final: 0.8747 (p) REVERT: E 273 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8201 (mtt180) REVERT: E 306 SER cc_start: 0.8766 (m) cc_final: 0.8246 (p) REVERT: E 498 PRO cc_start: 0.9022 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: D 530 MET cc_start: 0.8664 (mtp) cc_final: 0.8318 (mtp) REVERT: F 39 TYR cc_start: 0.9037 (m-80) cc_final: 0.8832 (m-80) REVERT: F 178 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7665 (ttm110) REVERT: F 426 MET cc_start: 0.7439 (mtp) cc_final: 0.6961 (mmp) REVERT: F 500 ARG cc_start: 0.6641 (mtt180) cc_final: 0.6203 (mtm-85) outliers start: 55 outliers final: 31 residues processed: 463 average time/residue: 0.2544 time to fit residues: 175.3278 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 : 1.604 ------------------------------------------------------------------------------- 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: 0.8980 chunk 182 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 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 = 0.3599 r_free = 0.3599 target = 0.147167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.123771 restraints weight = 23693.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.127323 restraints weight = 13317.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129685 restraints weight = 8968.885| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15532 Z= 0.211 Angle : 0.757 15.486 21253 Z= 0.365 Chirality : 0.049 0.349 2614 Planarity : 0.004 0.055 2601 Dihedral : 7.079 59.034 3440 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.22 % Rotamer: Outliers : 5.21 % Allowed : 15.42 % Favored : 79.38 % 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: 0.58 (0.20), residues: 1616 helix: 1.48 (0.27), residues: 388 sheet: 0.72 (0.24), residues: 421 loop : -0.28 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 479 HIS 0.007 0.001 HIS E 375 PHE 0.017 0.003 PHE E 354 TYR 0.020 0.002 TYR E 484 ARG 0.008 0.001 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 61) link_NAG-ASN : angle 3.05469 ( 183) link_BETA1-4 : bond 0.00617 ( 9) link_BETA1-4 : angle 3.02996 ( 27) hydrogen bonds : bond 0.05179 ( 475) hydrogen bonds : angle 5.41391 ( 1284) SS BOND : bond 0.00405 ( 33) SS BOND : angle 1.29823 ( 66) covalent geometry : bond 0.00488 (15429) covalent geometry : angle 0.69426 (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 466 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 389 time to evaluate : 1.728 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: 0.8873 (ttm) cc_final: 0.8416 (tpp) REVERT: A 176 PHE cc_start: 0.8649 (m-80) cc_final: 0.8436 (m-80) REVERT: A 177 TYR cc_start: 0.9261 (m-80) cc_final: 0.8828 (m-80) REVERT: A 192 ARG cc_start: 0.6770 (mpt-90) cc_final: 0.6077 (mpp80) REVERT: A 197 ASN cc_start: 0.7136 (p0) cc_final: 0.6698 (m110) REVERT: A 278 THR cc_start: 0.8957 (p) cc_final: 0.8494 (t) REVERT: A 474 ASP cc_start: 0.8373 (t70) cc_final: 0.7801 (p0) REVERT: A 484 TYR cc_start: 0.8950 (p90) cc_final: 0.8726 (p90) REVERT: B 626 MET cc_start: 0.7996 (ttt) cc_final: 0.7620 (ttm) REVERT: C 601 LYS cc_start: 0.8895 (mttp) cc_final: 0.8518 (mtpp) REVERT: E 35 TRP cc_start: 0.8659 (m100) cc_final: 0.8223 (m100) REVERT: E 102 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6916 (tm-30) REVERT: E 103 GLN cc_start: 0.9096 (tp40) cc_final: 0.8072 (tm-30) REVERT: E 121 LYS cc_start: 0.8223 (mmtt) cc_final: 0.8009 (tptt) REVERT: E 178 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7621 (tmm160) REVERT: E 273 ARG cc_start: 0.8693 (mtt90) cc_final: 0.8425 (mtt180) REVERT: E 306 SER cc_start: 0.8868 (m) cc_final: 0.8590 (p) REVERT: E 456 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7377 (ttp80) REVERT: F 97 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8435 (mmmm) REVERT: F 136 ASN cc_start: 0.7701 (t0) cc_final: 0.7429 (t0) REVERT: F 178 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7672 (ttm110) REVERT: F 379 CYS cc_start: 0.7759 (t) cc_final: 0.7548 (t) REVERT: F 426 MET cc_start: 0.7600 (mtp) cc_final: 0.7102 (mmp) outliers start: 77 outliers final: 51 residues processed: 430 average time/residue: 0.2666 time to fit residues: 171.1487 Evaluate side-chains 392 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 341 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.9980 chunk 24 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.147513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124403 restraints weight = 23703.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.128009 restraints weight = 13167.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.130410 restraints weight = 8784.050| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15532 Z= 0.146 Angle : 0.701 19.925 21253 Z= 0.330 Chirality : 0.048 0.366 2614 Planarity : 0.004 0.056 2601 Dihedral : 6.327 59.402 3436 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 4.67 % Allowed : 17.24 % Favored : 78.09 % 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: 0.65 (0.21), residues: 1616 helix: 1.91 (0.27), residues: 371 sheet: 0.66 (0.24), residues: 443 loop : -0.38 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.006 0.001 HIS A 374 PHE 0.017 0.002 PHE B 522 TYR 0.013 0.002 TYR A 173 ARG 0.007 0.001 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 61) link_NAG-ASN : angle 3.47156 ( 183) link_BETA1-4 : bond 0.00474 ( 9) link_BETA1-4 : angle 2.57047 ( 27) hydrogen bonds : bond 0.04640 ( 475) hydrogen bonds : angle 5.10781 ( 1284) SS BOND : bond 0.00300 ( 33) SS BOND : angle 1.03260 ( 66) covalent geometry : bond 0.00331 (15429) covalent geometry : angle 0.61677 (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 446 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 377 time to evaluate : 1.457 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 176 PHE cc_start: 0.8687 (m-80) cc_final: 0.8464 (m-80) REVERT: A 177 TYR cc_start: 0.9224 (m-80) cc_final: 0.8900 (m-80) REVERT: A 192 ARG cc_start: 0.6733 (mpt-90) cc_final: 0.5964 (mpp80) REVERT: A 195 ASN cc_start: 0.8231 (m110) cc_final: 0.7952 (t0) REVERT: A 197 ASN cc_start: 0.7068 (p0) cc_final: 0.6816 (m110) REVERT: A 278 THR cc_start: 0.8946 (p) cc_final: 0.8468 (t) REVERT: A 474 ASP cc_start: 0.8391 (t70) cc_final: 0.7827 (p0) REVERT: A 482 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7927 (mt-10) REVERT: A 484 TYR cc_start: 0.8862 (p90) cc_final: 0.8607 (p90) REVERT: B 626 MET cc_start: 0.7978 (ttt) cc_final: 0.7595 (ttm) REVERT: C 601 LYS cc_start: 0.8888 (mttp) cc_final: 0.8630 (mtpt) REVERT: E 35 TRP cc_start: 0.8705 (m100) cc_final: 0.8245 (m100) REVERT: E 102 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7100 (tm-30) REVERT: E 103 GLN cc_start: 0.9112 (tp40) cc_final: 0.8218 (tm-30) REVERT: E 178 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7611 (tmm160) REVERT: E 273 ARG cc_start: 0.8596 (mtt90) cc_final: 0.8337 (mtt180) REVERT: E 469 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7430 (ptp-110) REVERT: F 97 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8400 (mmmm) REVERT: F 136 ASN cc_start: 0.7683 (t0) cc_final: 0.7446 (t0) REVERT: F 153 GLU cc_start: 0.6449 (tp30) cc_final: 0.5754 (tp30) REVERT: F 178 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7597 (ttm110) REVERT: F 258 GLN cc_start: 0.9099 (mt0) cc_final: 0.8433 (mt0) REVERT: F 379 CYS cc_start: 0.7734 (t) cc_final: 0.7497 (t) REVERT: F 426 MET cc_start: 0.7682 (mtp) cc_final: 0.7193 (mmp) REVERT: F 432 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8101 (mm-40) outliers start: 69 outliers final: 56 residues processed: 407 average time/residue: 0.2507 time to fit residues: 151.9134 Evaluate side-chains 414 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 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 637 ASN Chi-restraints excluded: chain C residue 661 LEU 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 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 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 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 Chi-restraints excluded: chain F residue 494 LEU 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: 0.5980 chunk 103 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 145 optimal weight: 0.9980 overall best weight: 1.7382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121843 restraints weight = 24289.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125295 restraints weight = 13583.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.127624 restraints weight = 9155.870| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15532 Z= 0.202 Angle : 0.730 20.370 21253 Z= 0.348 Chirality : 0.049 0.378 2614 Planarity : 0.004 0.059 2601 Dihedral : 6.239 58.444 3436 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 5.61 % Allowed : 17.17 % 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: 0.45 (0.21), residues: 1616 helix: 1.66 (0.27), residues: 375 sheet: 0.55 (0.25), residues: 427 loop : -0.45 (0.21), residues: 814 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 0.015 0.002 PHE A 468 TYR 0.020 0.002 TYR F 173 ARG 0.008 0.001 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 61) link_NAG-ASN : angle 3.38072 ( 183) link_BETA1-4 : bond 0.00450 ( 9) link_BETA1-4 : angle 2.44698 ( 27) hydrogen bonds : bond 0.04728 ( 475) hydrogen bonds : angle 5.08730 ( 1284) SS BOND : bond 0.00406 ( 33) SS BOND : angle 1.41576 ( 66) covalent geometry : bond 0.00470 (15429) covalent geometry : angle 0.65275 (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 436 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 353 time to evaluate : 1.704 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 104 MET cc_start: 0.8859 (ttm) cc_final: 0.8632 (tpp) REVERT: A 176 PHE cc_start: 0.8678 (m-80) cc_final: 0.8476 (m-80) REVERT: A 177 TYR cc_start: 0.9289 (m-80) cc_final: 0.9006 (m-80) REVERT: A 190 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6421 (tm-30) REVERT: A 192 ARG cc_start: 0.6710 (mpt-90) cc_final: 0.6199 (mpt-90) REVERT: A 278 THR cc_start: 0.8999 (p) cc_final: 0.8463 (t) REVERT: A 414 ILE cc_start: 0.8510 (mt) cc_final: 0.8124 (tt) REVERT: A 474 ASP cc_start: 0.8465 (t70) cc_final: 0.7859 (p0) REVERT: A 482 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 484 TYR cc_start: 0.8889 (p90) cc_final: 0.8676 (p90) REVERT: A 486 TYR cc_start: 0.8777 (m-80) cc_final: 0.8492 (m-80) REVERT: B 626 MET cc_start: 0.8000 (ttt) cc_final: 0.7626 (ttm) REVERT: C 601 LYS cc_start: 0.8880 (mttp) cc_final: 0.8636 (mtpt) REVERT: E 35 TRP cc_start: 0.8759 (m100) cc_final: 0.8290 (m100) REVERT: E 103 GLN cc_start: 0.9179 (tp40) cc_final: 0.8400 (tm-30) REVERT: E 177 TYR cc_start: 0.8342 (m-80) cc_final: 0.7881 (m-80) REVERT: E 178 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7621 (tmm160) REVERT: E 273 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8169 (mtt180) REVERT: E 469 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7456 (ptp-110) REVERT: E 485 LYS cc_start: 0.9033 (ptpt) cc_final: 0.8803 (ptpp) REVERT: F 82 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: F 97 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8438 (mmmm) REVERT: F 136 ASN cc_start: 0.7762 (t0) cc_final: 0.7508 (t0) REVERT: F 178 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7609 (ttm110) REVERT: F 244 THR cc_start: 0.8873 (m) cc_final: 0.8297 (p) REVERT: F 258 GLN cc_start: 0.9049 (mt0) cc_final: 0.8400 (mt0) REVERT: F 426 MET cc_start: 0.7745 (mtp) cc_final: 0.7084 (mmt) REVERT: F 432 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8145 (mm-40) outliers start: 83 outliers final: 61 residues processed: 399 average time/residue: 0.2596 time to fit residues: 153.2736 Evaluate side-chains 399 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 336 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 180 ASP 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 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 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 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 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 120 VAL 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 Chi-restraints excluded: chain F residue 494 LEU 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: 0.4980 chunk 182 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 D 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.148238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125449 restraints weight = 23831.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128990 restraints weight = 13213.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131265 restraints weight = 8819.411| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15532 Z= 0.123 Angle : 0.680 20.116 21253 Z= 0.318 Chirality : 0.047 0.367 2614 Planarity : 0.004 0.060 2601 Dihedral : 6.061 59.760 3436 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.91 % Rotamer: Outliers : 4.46 % Allowed : 19.07 % Favored : 76.47 % 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: 0.46 (0.21), residues: 1616 helix: 1.80 (0.28), residues: 375 sheet: 0.53 (0.25), residues: 430 loop : -0.51 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.008 0.000 ARG E 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 61) link_NAG-ASN : angle 3.51375 ( 183) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 1.91363 ( 27) hydrogen bonds : bond 0.04252 ( 475) hydrogen bonds : angle 4.82560 ( 1284) SS BOND : bond 0.00265 ( 33) SS BOND : angle 1.28316 ( 66) covalent geometry : bond 0.00273 (15429) covalent geometry : angle 0.59273 (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 442 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 376 time to evaluate : 1.622 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 97 LYS cc_start: 0.9059 (mptt) cc_final: 0.8250 (tptp) REVERT: A 104 MET cc_start: 0.8806 (ttm) cc_final: 0.8595 (tpp) REVERT: A 177 TYR cc_start: 0.9229 (m-80) cc_final: 0.8987 (m-80) REVERT: A 190 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6656 (tm-30) REVERT: A 192 ARG cc_start: 0.6683 (mpt-90) cc_final: 0.6244 (mpt-90) REVERT: A 195 ASN cc_start: 0.8247 (m110) cc_final: 0.7211 (t0) REVERT: A 278 THR cc_start: 0.8899 (p) cc_final: 0.8331 (t) REVERT: A 414 ILE cc_start: 0.8586 (mt) cc_final: 0.8210 (tt) REVERT: A 474 ASP cc_start: 0.8532 (t70) cc_final: 0.7951 (p0) REVERT: A 475 MET cc_start: 0.8504 (mmm) cc_final: 0.8168 (mmm) REVERT: A 482 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 486 TYR cc_start: 0.8713 (m-80) cc_final: 0.8501 (m-80) REVERT: B 626 MET cc_start: 0.7927 (ttt) cc_final: 0.7572 (ttm) REVERT: C 601 LYS cc_start: 0.8881 (mttp) cc_final: 0.8669 (mtpt) REVERT: E 35 TRP cc_start: 0.8733 (m100) cc_final: 0.8251 (m100) REVERT: E 102 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7142 (tm-30) REVERT: E 103 GLN cc_start: 0.9140 (tp40) cc_final: 0.8431 (tm-30) REVERT: E 177 TYR cc_start: 0.8256 (m-80) cc_final: 0.7796 (m-80) REVERT: E 178 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7604 (tmm160) REVERT: E 273 ARG cc_start: 0.8498 (mtt90) cc_final: 0.8191 (mtt180) REVERT: E 469 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7502 (ptp-110) REVERT: F 82 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: F 136 ASN cc_start: 0.7773 (t0) cc_final: 0.7510 (t0) REVERT: F 258 GLN cc_start: 0.8985 (mt0) cc_final: 0.8386 (mt0) REVERT: F 426 MET cc_start: 0.7747 (mtp) cc_final: 0.7396 (mmp) outliers start: 66 outliers final: 54 residues processed: 410 average time/residue: 0.2535 time to fit residues: 155.3423 Evaluate side-chains 401 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 346 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU 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 B residue 540 GLN 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 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 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 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 627 THR 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 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 120 VAL 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 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: 6.9990 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: 0.7980 chunk 170 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN D 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.143689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120562 restraints weight = 24351.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.124075 restraints weight = 13464.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.126425 restraints weight = 9010.983| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15532 Z= 0.210 Angle : 0.746 22.051 21253 Z= 0.350 Chirality : 0.051 0.717 2614 Planarity : 0.004 0.061 2601 Dihedral : 6.307 58.182 3436 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.53 % Favored : 96.35 % Rotamer: Outliers : 5.48 % Allowed : 18.32 % Favored : 76.20 % 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: 0.16 (0.21), residues: 1616 helix: 1.60 (0.27), residues: 375 sheet: 0.20 (0.24), residues: 435 loop : -0.62 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 45 HIS 0.006 0.001 HIS E 375 PHE 0.023 0.002 PHE A 391 TYR 0.013 0.002 TYR F 173 ARG 0.009 0.001 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00774 ( 61) link_NAG-ASN : angle 3.68591 ( 183) link_BETA1-4 : bond 0.00454 ( 9) link_BETA1-4 : angle 2.13030 ( 27) hydrogen bonds : bond 0.04664 ( 475) hydrogen bonds : angle 4.97923 ( 1284) SS BOND : bond 0.00402 ( 33) SS BOND : angle 1.13427 ( 66) covalent geometry : bond 0.00487 (15429) covalent geometry : angle 0.66034 (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 430 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 349 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8881 (ttm) cc_final: 0.8660 (tpp) REVERT: A 177 TYR cc_start: 0.9272 (m-80) cc_final: 0.9036 (m-80) REVERT: A 190 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6519 (tm-30) REVERT: A 192 ARG cc_start: 0.6500 (mpt-90) cc_final: 0.5875 (mpt-90) REVERT: A 278 THR cc_start: 0.8942 (p) cc_final: 0.8442 (t) REVERT: A 325 ASP cc_start: 0.7969 (t0) cc_final: 0.7722 (t0) REVERT: A 414 ILE cc_start: 0.8570 (mt) cc_final: 0.8216 (tt) REVERT: A 474 ASP cc_start: 0.8537 (t70) cc_final: 0.7805 (p0) REVERT: A 482 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8114 (mt-10) REVERT: A 486 TYR cc_start: 0.8862 (m-80) cc_final: 0.8653 (m-80) REVERT: B 626 MET cc_start: 0.8023 (ttt) cc_final: 0.7722 (ttm) REVERT: C 601 LYS cc_start: 0.8945 (mttp) cc_final: 0.8688 (mtpt) REVERT: E 35 TRP cc_start: 0.8790 (m100) cc_final: 0.8310 (m100) REVERT: E 178 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7551 (tmm160) REVERT: E 469 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.7495 (ptp-110) REVERT: E 485 LYS cc_start: 0.9016 (ptpt) cc_final: 0.8763 (ptpp) REVERT: D 540 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: F 82 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: F 136 ASN cc_start: 0.7804 (t0) cc_final: 0.7587 (t0) REVERT: F 258 GLN cc_start: 0.9074 (mt0) cc_final: 0.8335 (mt0) REVERT: F 426 MET cc_start: 0.7786 (mtp) cc_final: 0.7194 (mmt) REVERT: F 432 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8184 (mm-40) outliers start: 81 outliers final: 66 residues processed: 394 average time/residue: 0.2553 time to fit residues: 150.6720 Evaluate side-chains 405 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 336 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 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 322 ASP 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 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 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 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 138 ILE 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 450 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN 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 627 THR 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 51 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 120 VAL 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 268 GLU 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=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: 1.9990 chunk 74 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.146831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124024 restraints weight = 23794.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127538 restraints weight = 13298.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129900 restraints weight = 8923.096| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 15532 Z= 0.138 Angle : 0.696 19.617 21253 Z= 0.329 Chirality : 0.049 0.669 2614 Planarity : 0.004 0.060 2601 Dihedral : 6.112 59.922 3436 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 4.53 % Allowed : 19.54 % Favored : 75.93 % 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: 0.27 (0.21), residues: 1616 helix: 1.75 (0.28), residues: 375 sheet: 0.31 (0.24), residues: 442 loop : -0.63 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 339 HIS 0.003 0.001 HIS F 72 PHE 0.023 0.002 PHE A 391 TYR 0.013 0.001 TYR E 318 ARG 0.010 0.001 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 61) link_NAG-ASN : angle 3.36793 ( 183) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 1.72352 ( 27) hydrogen bonds : bond 0.04291 ( 475) hydrogen bonds : angle 4.80464 ( 1284) SS BOND : bond 0.00371 ( 33) SS BOND : angle 1.63230 ( 66) covalent geometry : bond 0.00318 (15429) covalent geometry : angle 0.61644 (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 426 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 359 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8977 (mptt) cc_final: 0.8216 (tptp) REVERT: A 190 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 192 ARG cc_start: 0.6570 (mpt-90) cc_final: 0.6032 (mpt-90) REVERT: A 278 THR cc_start: 0.8886 (p) cc_final: 0.8329 (t) REVERT: A 325 ASP cc_start: 0.7921 (t0) cc_final: 0.7718 (t0) REVERT: A 414 ILE cc_start: 0.8576 (mt) cc_final: 0.8256 (tt) REVERT: A 474 ASP cc_start: 0.8522 (t70) cc_final: 0.7802 (p0) REVERT: A 482 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7943 (mt-10) REVERT: A 486 TYR cc_start: 0.8773 (m-80) cc_final: 0.8526 (m-80) REVERT: B 626 MET cc_start: 0.7982 (ttt) cc_final: 0.7603 (ttm) REVERT: C 601 LYS cc_start: 0.8921 (mttp) cc_final: 0.8701 (mtpt) REVERT: E 35 TRP cc_start: 0.8747 (m100) cc_final: 0.8311 (m100) REVERT: E 103 GLN cc_start: 0.9206 (tp40) cc_final: 0.8565 (tm-30) REVERT: E 177 TYR cc_start: 0.8239 (m-80) cc_final: 0.7850 (m-80) REVERT: E 178 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7550 (tmm160) REVERT: E 469 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7556 (ptp-110) REVERT: E 485 LYS cc_start: 0.8880 (ptpt) cc_final: 0.8661 (ptpp) REVERT: F 82 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: F 136 ASN cc_start: 0.7805 (t0) cc_final: 0.7564 (t0) REVERT: F 178 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7379 (ttm110) REVERT: F 258 GLN cc_start: 0.9011 (mt0) cc_final: 0.8459 (mt0) REVERT: F 426 MET cc_start: 0.7633 (mtp) cc_final: 0.7322 (mmp) outliers start: 67 outliers final: 58 residues processed: 394 average time/residue: 0.2683 time to fit residues: 157.3071 Evaluate side-chains 410 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 351 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 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 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 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 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 356 ASN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain D residue 523 LEU 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 627 THR 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 51 THR 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 120 VAL 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 269 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 82 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.122934 restraints weight = 23831.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.126412 restraints weight = 13409.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128730 restraints weight = 9020.379| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15532 Z= 0.152 Angle : 0.706 19.552 21253 Z= 0.334 Chirality : 0.049 0.600 2614 Planarity : 0.004 0.062 2601 Dihedral : 6.078 59.707 3434 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 4.39 % Allowed : 20.15 % Favored : 75.46 % 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: 0.23 (0.21), residues: 1616 helix: 1.73 (0.28), residues: 376 sheet: 0.27 (0.24), residues: 432 loop : -0.64 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 69 HIS 0.004 0.001 HIS E 375 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 0.00566 ( 61) link_NAG-ASN : angle 3.36335 ( 183) link_BETA1-4 : bond 0.00423 ( 9) link_BETA1-4 : angle 1.75286 ( 27) hydrogen bonds : bond 0.04304 ( 475) hydrogen bonds : angle 4.73689 ( 1284) SS BOND : bond 0.00370 ( 33) SS BOND : angle 1.57614 ( 66) covalent geometry : bond 0.00355 (15429) covalent geometry : angle 0.62859 (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 424 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 359 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8994 (mptt) cc_final: 0.8215 (tptp) REVERT: A 104 MET cc_start: 0.8754 (ttm) cc_final: 0.8432 (tpp) REVERT: A 177 TYR cc_start: 0.9213 (m-80) cc_final: 0.8953 (m-80) REVERT: A 190 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6590 (tm-30) REVERT: A 192 ARG cc_start: 0.6563 (mpt-90) cc_final: 0.5980 (mpt-90) REVERT: A 278 THR cc_start: 0.8872 (p) cc_final: 0.8335 (t) REVERT: A 352 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7670 (t-90) REVERT: A 414 ILE cc_start: 0.8565 (mt) cc_final: 0.8269 (tt) REVERT: A 422 GLN cc_start: 0.8177 (mt0) cc_final: 0.7795 (mt0) REVERT: A 474 ASP cc_start: 0.8508 (t70) cc_final: 0.7767 (p0) REVERT: A 475 MET cc_start: 0.8531 (mmm) cc_final: 0.8198 (mmm) REVERT: A 482 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 486 TYR cc_start: 0.8788 (m-80) cc_final: 0.8543 (m-80) REVERT: B 626 MET cc_start: 0.7970 (ttt) cc_final: 0.7654 (ttm) REVERT: C 601 LYS cc_start: 0.8915 (mttp) cc_final: 0.8699 (mtpt) REVERT: C 626 MET cc_start: 0.7556 (ttm) cc_final: 0.7339 (mtp) REVERT: E 35 TRP cc_start: 0.8760 (m100) cc_final: 0.8324 (m100) REVERT: E 103 GLN cc_start: 0.9218 (tp40) cc_final: 0.8654 (tm-30) REVERT: E 177 TYR cc_start: 0.8261 (m-80) cc_final: 0.7865 (m-80) REVERT: E 178 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7528 (tmm160) REVERT: E 457 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7294 (t70) REVERT: E 469 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.7570 (ptp-110) REVERT: E 485 LYS cc_start: 0.8898 (ptpt) cc_final: 0.8681 (ptpp) REVERT: F 82 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: F 136 ASN cc_start: 0.7796 (t0) cc_final: 0.7543 (t0) REVERT: F 178 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7372 (ttm110) REVERT: F 244 THR cc_start: 0.8856 (m) cc_final: 0.8305 (p) REVERT: F 258 GLN cc_start: 0.9020 (mt0) cc_final: 0.8331 (mt0) REVERT: F 290 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8416 (mt-10) REVERT: F 426 MET cc_start: 0.7634 (mtp) cc_final: 0.7276 (mmp) REVERT: F 432 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8191 (mm-40) outliers start: 65 outliers final: 57 residues processed: 392 average time/residue: 0.2602 time to fit residues: 151.0696 Evaluate side-chains 402 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 341 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 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 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 632 ASP 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 637 ASN Chi-restraints excluded: chain C residue 661 LEU 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 270 VAL Chi-restraints excluded: chain E residue 271 ILE 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 457 ASP Chi-restraints excluded: chain D residue 523 LEU 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 627 THR 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 51 THR 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 120 VAL 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 269 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: 0.3980 chunk 160 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 425 ASN ** 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 = 0.3604 r_free = 0.3604 target = 0.147360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124249 restraints weight = 23998.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127765 restraints weight = 13424.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130149 restraints weight = 9017.259| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15532 Z= 0.129 Angle : 0.690 19.265 21253 Z= 0.327 Chirality : 0.048 0.563 2614 Planarity : 0.004 0.062 2601 Dihedral : 5.948 59.493 3434 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 4.19 % Allowed : 20.89 % 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: 0.25 (0.21), residues: 1616 helix: 1.75 (0.28), residues: 375 sheet: 0.31 (0.24), residues: 428 loop : -0.64 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 339 HIS 0.004 0.001 HIS F 375 PHE 0.020 0.001 PHE A 391 TYR 0.014 0.001 TYR E 318 ARG 0.010 0.001 ARG E 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 61) link_NAG-ASN : angle 3.29816 ( 183) link_BETA1-4 : bond 0.00442 ( 9) link_BETA1-4 : angle 1.60208 ( 27) hydrogen bonds : bond 0.04161 ( 475) hydrogen bonds : angle 4.62758 ( 1284) SS BOND : bond 0.00333 ( 33) SS BOND : angle 1.65604 ( 66) covalent geometry : bond 0.00295 (15429) covalent geometry : angle 0.61229 (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 416 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 354 time to evaluate : 1.495 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 97 LYS cc_start: 0.8988 (mptt) cc_final: 0.8166 (tptp) REVERT: A 104 MET cc_start: 0.8685 (ttm) cc_final: 0.8320 (tpp) REVERT: A 177 TYR cc_start: 0.9233 (m-80) cc_final: 0.8979 (m-80) REVERT: A 190 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6634 (tm-30) REVERT: A 192 ARG cc_start: 0.6553 (mpt-90) cc_final: 0.6020 (mpt-90) REVERT: A 278 THR cc_start: 0.8870 (p) cc_final: 0.8281 (t) REVERT: A 352 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7617 (t-90) REVERT: A 414 ILE cc_start: 0.8597 (mt) cc_final: 0.8331 (tt) REVERT: A 422 GLN cc_start: 0.8211 (mt0) cc_final: 0.7772 (mt0) REVERT: A 466 GLU cc_start: 0.6517 (pp20) cc_final: 0.5883 (pp20) REVERT: A 474 ASP cc_start: 0.8549 (t70) cc_final: 0.7721 (p0) REVERT: A 475 MET cc_start: 0.8448 (mmm) cc_final: 0.8033 (mmm) REVERT: A 482 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7985 (mt-10) REVERT: A 486 TYR cc_start: 0.8743 (m-80) cc_final: 0.8510 (m-80) REVERT: B 540 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8644 (mt0) REVERT: B 626 MET cc_start: 0.7977 (ttt) cc_final: 0.7641 (ttm) REVERT: E 35 TRP cc_start: 0.8746 (m100) cc_final: 0.8288 (m100) REVERT: E 103 GLN cc_start: 0.9194 (tp40) cc_final: 0.8584 (tm-30) REVERT: E 177 TYR cc_start: 0.8259 (m-80) cc_final: 0.7854 (m-80) REVERT: E 178 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7515 (tmm160) REVERT: E 457 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7367 (t70) REVERT: E 469 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7603 (ptp-110) REVERT: F 82 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: F 136 ASN cc_start: 0.7844 (t0) cc_final: 0.7602 (t0) REVERT: F 258 GLN cc_start: 0.8986 (mt0) cc_final: 0.8404 (mt0) REVERT: F 290 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8386 (mt-10) REVERT: F 426 MET cc_start: 0.7618 (mtp) cc_final: 0.7287 (mmp) outliers start: 62 outliers final: 55 residues processed: 384 average time/residue: 0.2628 time to fit residues: 149.6979 Evaluate side-chains 403 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 345 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 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 173 TYR 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 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 632 ASP 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 637 ASN Chi-restraints excluded: chain C residue 661 LEU 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 270 VAL Chi-restraints excluded: chain E residue 271 ILE 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 457 ASP Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 593 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 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 51 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** 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 = 0.3602 r_free = 0.3602 target = 0.147114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124361 restraints weight = 24026.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127829 restraints weight = 13437.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130187 restraints weight = 9038.621| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15532 Z= 0.133 Angle : 0.678 19.072 21253 Z= 0.321 Chirality : 0.048 0.521 2614 Planarity : 0.004 0.062 2601 Dihedral : 5.849 58.599 3434 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 4.12 % Allowed : 21.03 % Favored : 74.85 % 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: 0.29 (0.21), residues: 1616 helix: 1.79 (0.28), residues: 375 sheet: 0.33 (0.24), residues: 430 loop : -0.63 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 631 HIS 0.004 0.001 HIS F 375 PHE 0.018 0.001 PHE A 391 TYR 0.015 0.001 TYR E 318 ARG 0.010 0.001 ARG E 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 61) link_NAG-ASN : angle 3.18366 ( 183) link_BETA1-4 : bond 0.00442 ( 9) link_BETA1-4 : angle 1.57326 ( 27) hydrogen bonds : bond 0.04098 ( 475) hydrogen bonds : angle 4.57551 ( 1284) SS BOND : bond 0.00319 ( 33) SS BOND : angle 1.57381 ( 66) covalent geometry : bond 0.00308 (15429) covalent geometry : angle 0.60495 (20977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5159.58 seconds wall clock time: 90 minutes 14.94 seconds (5414.94 seconds total)