Starting phenix.real_space_refine on Mon Nov 18 01:58:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swx_40824/11_2024/8swx_40824.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swx_40824/11_2024/8swx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swx_40824/11_2024/8swx_40824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swx_40824/11_2024/8swx_40824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swx_40824/11_2024/8swx_40824.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swx_40824/11_2024/8swx_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-5513/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: 10.08, per 1000 atoms: 0.66 Number of scatterers: 15170 At special positions: 0 Unit cell: (134.03, 123.72, 148.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3024 8.00 N 2592 7.00 C 9452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.08 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.12 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 332 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 445 " distance=2.10 Simple disulfide: pdb=" SG CYS E 386 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.05 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.07 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.05 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 332 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 386 " - pdb=" SG CYS F 418 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 241 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 355 " " NAG A 611 " - " ASN A 363 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 448 " " NAG A 614 " - " ASN A 295 " " NAG A 615 " - " ASN A 289 " " NAG A 616 " - " ASN A 339 " " NAG A 617 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 241 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 333 " " NAG E 609 " - " ASN E 340 " " NAG E 610 " - " ASN E 364 " " NAG E 611 " - " ASN E 448 " " NAG E 612 " - " ASN E 133 " " NAG E 613 " - " ASN E 295 " " NAG E 614 " - " ASN E 356 " " NAG E 615 " - " ASN E 387 " " NAG E 616 " - " ASN E 393 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 241 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 289 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 333 " " NAG F 612 " - " ASN F 340 " " NAG F 613 " - " ASN F 387 " " NAG F 614 " - " ASN F 448 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN E 156 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN F 262 " Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3526 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 27 sheets defined 26.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 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: 5.09 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3196 1.32 - 1.46: 4745 1.46 - 1.59: 7287 1.59 - 1.73: 71 1.73 - 1.87: 130 Bond restraints: 15429 Sorted by residual: bond pdb=" CB HIS E 375 " pdb=" CG HIS E 375 " ideal model delta sigma weight residual 1.497 1.372 0.125 1.40e-02 5.10e+03 7.94e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.57e+01 bond pdb=" CD2 TRP B 571 " pdb=" CE3 TRP B 571 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.29e+01 bond pdb=" CZ2 TRP C 571 " pdb=" CH2 TRP C 571 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.12e+01 bond pdb=" CZ2 TRP B 571 " pdb=" CH2 TRP B 571 " ideal model delta sigma weight residual 1.368 1.488 -0.120 1.90e-02 2.77e+03 4.00e+01 ... (remaining 15424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 18771 2.68 - 5.36: 1979 5.36 - 8.04: 211 8.04 - 10.72: 14 10.72 - 13.40: 2 Bond angle restraints: 20977 Sorted by residual: angle pdb=" C PHE F 233 " pdb=" N ASN F 234 " pdb=" CA ASN F 234 " ideal model delta sigma weight residual 120.28 133.68 -13.40 1.34e+00 5.57e-01 1.00e+02 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.76 -8.20 1.01e+00 9.80e-01 6.59e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.87 128.27 -8.40 1.04e+00 9.25e-01 6.53e+01 angle pdb=" N GLU A 87 " pdb=" CA GLU A 87 " pdb=" C GLU A 87 " ideal model delta sigma weight residual 111.36 119.87 -8.51 1.09e+00 8.42e-01 6.09e+01 angle pdb=" N CYS E 196 " pdb=" CA CYS E 196 " pdb=" C CYS E 196 " ideal model delta sigma weight residual 113.43 103.62 9.81 1.26e+00 6.30e-01 6.06e+01 ... (remaining 20972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 9899 21.13 - 42.25: 209 42.25 - 63.38: 64 63.38 - 84.51: 23 84.51 - 105.64: 14 Dihedral angle restraints: 10209 sinusoidal: 4798 harmonic: 5411 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual 93.00 151.82 -58.82 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.24 40.24 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.88 39.88 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 10206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1716 0.099 - 0.198: 556 0.198 - 0.297: 168 0.297 - 0.396: 108 0.396 - 0.495: 66 Chirality restraints: 2614 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.38e+02 ... (remaining 2611 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " 0.082 2.00e-02 2.50e+03 8.87e-02 9.84e+01 pdb=" CG ASN A 392 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " -0.140 2.00e-02 2.50e+03 pdb=" C1 NAG A 617 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 160 " 0.082 2.00e-02 2.50e+03 8.65e-02 9.36e+01 pdb=" CG ASN F 160 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN F 160 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN F 160 " -0.134 2.00e-02 2.50e+03 pdb=" C1 NAG F 602 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 393 " -0.068 2.00e-02 2.50e+03 7.09e-02 6.29e+01 pdb=" CG ASN E 393 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 393 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 393 " 0.110 2.00e-02 2.50e+03 pdb=" C1 NAG E 616 " -0.086 2.00e-02 2.50e+03 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3524 2.80 - 3.32: 13801 3.32 - 3.85: 24160 3.85 - 4.37: 29274 4.37 - 4.90: 46462 Nonbonded interactions: 117221 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.272 3.040 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.391 3.120 nonbonded pdb=" OD2 ASP C 632 " pdb=" NZ LYS E 46 " model vdw 2.399 3.120 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.407 2.496 nonbonded pdb=" OE2 GLU E 83 " pdb=" NZ LYS E 227 " model vdw 2.418 3.120 ... (remaining 117216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 66 through 395 or resid 412 through \ 504 or resid 601 through 614)) selection = (chain 'E' and (resid 33 through 182 or resid 189 through 396 or resid 412 throu \ gh 457 or resid 465 through 504 or resid 601 through 614)) selection = (chain 'F' and (resid 33 through 182 or resid 189 through 396 or resid 412 throu \ gh 464 or resid 466 through 504 or resid 601 through 614)) } ncs_group { reference = (chain 'B' and (resid 522 through 663 or resid 702 through 703)) selection = chain 'C' selection = (chain 'D' and (resid 522 through 663 or resid 702 through 703)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.360 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- 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 15429 Z= 1.357 Angle : 1.694 13.400 20977 Z= 1.099 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 *********************** 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 : 1.521 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: 0.2837 time to fit residues: 255.4468 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 : 1.590 ------------------------------------------------------------------------------- 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: 0.9980 chunk 106 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 656 ASN E 103 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15429 Z= 0.249 Angle : 0.732 9.705 20977 Z= 0.372 Chirality : 0.050 0.367 2614 Planarity : 0.004 0.054 2601 Dihedral : 7.905 69.237 3440 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.29 % Favored : 97.65 % 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: 0.91 (0.20), residues: 1616 helix: 1.75 (0.27), residues: 382 sheet: 0.85 (0.24), residues: 432 loop : -0.03 (0.21), residues: 802 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 0.027 0.003 PHE F 468 TYR 0.022 0.002 TYR F 173 ARG 0.011 0.001 ARG F 178 *********************** 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 490 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 435 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8614 (tptp) REVERT: A 256 SER cc_start: 0.9481 (p) cc_final: 0.9198 (t) REVERT: A 278 THR cc_start: 0.8511 (p) cc_final: 0.8025 (t) REVERT: A 356 ASN cc_start: 0.8583 (p0) cc_final: 0.8307 (p0) REVERT: A 474 ASP cc_start: 0.8222 (t70) cc_final: 0.7874 (p0) REVERT: A 484 TYR cc_start: 0.9058 (p90) cc_final: 0.8718 (p90) REVERT: B 607 ASN cc_start: 0.8460 (p0) cc_final: 0.8217 (p0) REVERT: B 621 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7566 (mt-10) REVERT: B 626 MET cc_start: 0.7947 (ttt) cc_final: 0.7671 (ttm) REVERT: B 652 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7154 (tm-30) REVERT: B 653 GLN cc_start: 0.7855 (mt0) cc_final: 0.7649 (mt0) REVERT: C 601 LYS cc_start: 0.8768 (mttp) cc_final: 0.8465 (mtpp) REVERT: C 645 LEU cc_start: 0.9193 (mt) cc_final: 0.8972 (mt) REVERT: E 35 TRP cc_start: 0.8469 (m100) cc_final: 0.8255 (m100) REVERT: E 102 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7253 (tm-30) REVERT: E 178 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7834 (ttp80) REVERT: E 306 SER cc_start: 0.8768 (m) cc_final: 0.8342 (p) REVERT: E 491 ILE cc_start: 0.9068 (mm) cc_final: 0.8782 (tp) REVERT: E 498 PRO cc_start: 0.9064 (Cg_endo) cc_final: 0.8804 (Cg_exo) REVERT: D 530 MET cc_start: 0.8564 (mtp) cc_final: 0.8335 (mtp) REVERT: D 587 LEU cc_start: 0.9638 (mt) cc_final: 0.9338 (mt) REVERT: F 426 MET cc_start: 0.7697 (mtp) cc_final: 0.7083 (mmp) REVERT: F 500 ARG cc_start: 0.7392 (mtt180) cc_final: 0.6734 (mtm-85) outliers start: 55 outliers final: 32 residues processed: 469 average time/residue: 0.2799 time to fit residues: 194.9239 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 : 1.582 ------------------------------------------------------------------------------- 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 180 ASP 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 A residue 446 VAL 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 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 391 LEU 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 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 216 HIS A 422 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 195 ASN D 656 ASN F 170 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15429 Z= 0.371 Angle : 0.756 9.144 20977 Z= 0.382 Chirality : 0.051 0.356 2614 Planarity : 0.005 0.057 2601 Dihedral : 7.191 57.661 3436 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 5.27 % Allowed : 14.74 % Favored : 79.99 % 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: 0.35 (0.20), residues: 1616 helix: 1.41 (0.27), residues: 376 sheet: 0.50 (0.25), residues: 420 loop : -0.42 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 45 HIS 0.008 0.001 HIS E 375 PHE 0.020 0.003 PHE D 522 TYR 0.025 0.002 TYR E 484 ARG 0.018 0.001 ARG F 178 *********************** 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 453 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 375 time to evaluate : 1.772 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: 0.8889 (ttm) cc_final: 0.8446 (tpp) REVERT: A 160 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7091 (m110) REVERT: A 176 PHE cc_start: 0.8790 (m-80) cc_final: 0.8589 (m-80) REVERT: A 278 THR cc_start: 0.8727 (p) cc_final: 0.8228 (t) REVERT: A 474 ASP cc_start: 0.8455 (t70) cc_final: 0.7833 (p0) REVERT: B 540 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.8911 (mp-120) REVERT: B 626 MET cc_start: 0.8073 (ttt) cc_final: 0.7827 (ttm) REVERT: E 35 TRP cc_start: 0.8630 (m100) cc_final: 0.8387 (m100) REVERT: E 103 GLN cc_start: 0.9157 (tp40) cc_final: 0.8387 (tm-30) REVERT: E 121 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8167 (tptt) REVERT: E 178 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7814 (tmm160) REVERT: E 456 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7474 (ttp80) REVERT: E 491 ILE cc_start: 0.9071 (mm) cc_final: 0.8809 (tp) REVERT: D 530 MET cc_start: 0.8333 (mtp) cc_final: 0.7992 (mtp) REVERT: F 111 LEU cc_start: 0.9167 (tp) cc_final: 0.8864 (tp) REVERT: F 426 MET cc_start: 0.7885 (mtp) cc_final: 0.7209 (mmp) REVERT: F 432 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8132 (mm-40) REVERT: F 481 SER cc_start: 0.8449 (p) cc_final: 0.8167 (p) outliers start: 78 outliers final: 52 residues processed: 417 average time/residue: 0.2686 time to fit residues: 166.3932 Evaluate side-chains 384 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 329 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 257 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 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 123 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 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 365 SER Chi-restraints excluded: chain E residue 394 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 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 123 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 432 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 10.0000 chunk 125 optimal weight: 0.0060 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 348 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15429 Z= 0.375 Angle : 0.719 8.675 20977 Z= 0.360 Chirality : 0.050 0.373 2614 Planarity : 0.004 0.060 2601 Dihedral : 6.878 57.052 3436 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 5.81 % Allowed : 16.90 % Favored : 77.28 % 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: 0.13 (0.20), residues: 1616 helix: 1.27 (0.27), residues: 377 sheet: 0.34 (0.25), residues: 412 loop : -0.56 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 45 HIS 0.006 0.001 HIS A 374 PHE 0.020 0.002 PHE B 522 TYR 0.016 0.002 TYR A 191 ARG 0.008 0.001 ARG A 469 *********************** 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 434 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 348 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.9110 (m-80) cc_final: 0.8877 (m-80) REVERT: A 197 ASN cc_start: 0.7090 (p0) cc_final: 0.6778 (m110) REVERT: A 278 THR cc_start: 0.8783 (p) cc_final: 0.8266 (t) REVERT: A 474 ASP cc_start: 0.8565 (t70) cc_final: 0.7816 (p0) REVERT: B 540 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8963 (mp-120) REVERT: B 626 MET cc_start: 0.8051 (ttt) cc_final: 0.7821 (ttm) REVERT: E 35 TRP cc_start: 0.8730 (m100) cc_final: 0.7758 (m100) REVERT: E 103 GLN cc_start: 0.9192 (tp40) cc_final: 0.8555 (tm-30) REVERT: E 178 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7815 (tmm160) REVERT: E 491 ILE cc_start: 0.9095 (mm) cc_final: 0.8775 (tp) REVERT: D 530 MET cc_start: 0.8448 (mtp) cc_final: 0.8144 (mtp) REVERT: D 534 SER cc_start: 0.9148 (p) cc_final: 0.8919 (p) REVERT: F 82 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: F 111 LEU cc_start: 0.9184 (tp) cc_final: 0.8956 (tp) REVERT: F 426 MET cc_start: 0.7934 (mtp) cc_final: 0.7041 (mmt) REVERT: F 501 CYS cc_start: 0.7903 (t) cc_final: 0.7679 (t) outliers start: 86 outliers final: 66 residues processed: 398 average time/residue: 0.2619 time to fit residues: 155.3285 Evaluate side-chains 391 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 323 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 322 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain 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 365 SER Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 394 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 606 THR Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 663 LEU 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 125 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 128 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 274 SER 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 147 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 158 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** C 630 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15429 Z= 0.201 Angle : 0.612 7.444 20977 Z= 0.309 Chirality : 0.047 0.389 2614 Planarity : 0.004 0.057 2601 Dihedral : 6.318 59.075 3436 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 4.73 % Allowed : 18.53 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.20), residues: 1616 helix: 1.73 (0.28), residues: 369 sheet: 0.26 (0.24), residues: 440 loop : -0.58 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.002 PHE A 376 TYR 0.020 0.001 TYR F 173 ARG 0.010 0.001 ARG F 178 *********************** 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 424 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 354 time to evaluate : 1.492 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: 0.8601 (m-90) cc_final: 0.8302 (m-90) REVERT: A 104 MET cc_start: 0.8856 (ttm) cc_final: 0.8608 (tpp) REVERT: A 249 HIS cc_start: 0.8951 (p-80) cc_final: 0.8654 (p-80) REVERT: A 278 THR cc_start: 0.8655 (p) cc_final: 0.8157 (t) REVERT: A 474 ASP cc_start: 0.8477 (t70) cc_final: 0.7800 (p0) REVERT: B 626 MET cc_start: 0.7973 (ttt) cc_final: 0.7690 (ttm) REVERT: E 103 GLN cc_start: 0.9174 (tp40) cc_final: 0.8618 (tm-30) REVERT: E 178 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7747 (tmm160) REVERT: E 491 ILE cc_start: 0.9080 (mm) cc_final: 0.8764 (tp) REVERT: D 534 SER cc_start: 0.9135 (p) cc_final: 0.8889 (p) REVERT: F 258 GLN cc_start: 0.8733 (mt0) cc_final: 0.8333 (tt0) REVERT: F 426 MET cc_start: 0.7879 (mtp) cc_final: 0.7257 (mmp) outliers start: 70 outliers final: 53 residues processed: 390 average time/residue: 0.2593 time to fit residues: 151.2535 Evaluate side-chains 386 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 333 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 618 ASN 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 161 MET 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 E residue 481 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 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 443 ILE 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 59 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 0.0020 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 630 GLN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15429 Z= 0.253 Angle : 0.627 9.170 20977 Z= 0.314 Chirality : 0.048 0.371 2614 Planarity : 0.004 0.060 2601 Dihedral : 6.247 57.678 3436 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 5.14 % Allowed : 18.66 % Favored : 76.20 % 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: 0.14 (0.20), residues: 1616 helix: 1.63 (0.28), residues: 375 sheet: 0.05 (0.24), residues: 437 loop : -0.58 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 35 HIS 0.004 0.001 HIS E 375 PHE 0.011 0.002 PHE B 522 TYR 0.015 0.002 TYR F 173 ARG 0.013 0.001 ARG F 178 *********************** 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 431 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 355 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8579 (m-90) cc_final: 0.8306 (m-90) REVERT: A 104 MET cc_start: 0.8856 (ttm) cc_final: 0.8623 (tpp) REVERT: A 177 TYR cc_start: 0.9093 (m-80) cc_final: 0.8887 (m-80) REVERT: A 278 THR cc_start: 0.8716 (p) cc_final: 0.8174 (t) REVERT: A 474 ASP cc_start: 0.8598 (t70) cc_final: 0.7778 (p0) REVERT: B 626 MET cc_start: 0.8003 (ttt) cc_final: 0.7784 (ttm) REVERT: E 103 GLN cc_start: 0.9205 (tp40) cc_final: 0.8732 (tm-30) REVERT: E 177 TYR cc_start: 0.8257 (m-80) cc_final: 0.7910 (m-80) REVERT: E 178 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7715 (tmm160) REVERT: E 491 ILE cc_start: 0.9086 (mm) cc_final: 0.8774 (tp) REVERT: D 530 MET cc_start: 0.8480 (mtp) cc_final: 0.8194 (mtp) REVERT: D 534 SER cc_start: 0.9157 (p) cc_final: 0.8915 (p) REVERT: D 540 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: F 82 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: F 111 LEU cc_start: 0.9191 (tp) cc_final: 0.8922 (tp) REVERT: F 258 GLN cc_start: 0.8744 (mt0) cc_final: 0.8519 (tt0) REVERT: F 290 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8405 (mt-10) REVERT: F 426 MET cc_start: 0.7941 (mtp) cc_final: 0.7309 (mmt) outliers start: 76 outliers final: 60 residues processed: 398 average time/residue: 0.2642 time to fit residues: 156.5808 Evaluate side-chains 399 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 337 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 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 443 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 622 ILE 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 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 365 SER Chi-restraints excluded: chain E residue 391 LEU 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 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 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 274 SER Chi-restraints excluded: chain F residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 630 GLN E 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 15429 Z= 0.256 Angle : 0.643 16.084 20977 Z= 0.321 Chirality : 0.048 0.373 2614 Planarity : 0.004 0.061 2601 Dihedral : 6.253 59.228 3436 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.65 % Favored : 96.23 % Rotamer: Outliers : 5.14 % Allowed : 20.01 % 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: 0.09 (0.21), residues: 1616 helix: 1.51 (0.28), residues: 380 sheet: 0.06 (0.24), residues: 445 loop : -0.61 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 35 HIS 0.007 0.001 HIS A 249 PHE 0.010 0.002 PHE F 377 TYR 0.015 0.001 TYR E 318 ARG 0.010 0.001 ARG A 456 *********************** 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 428 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 352 time to evaluate : 1.699 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 69 TRP cc_start: 0.8586 (m-90) cc_final: 0.8347 (m-90) REVERT: A 278 THR cc_start: 0.8697 (p) cc_final: 0.8134 (t) REVERT: A 474 ASP cc_start: 0.8636 (t70) cc_final: 0.7792 (p0) REVERT: B 626 MET cc_start: 0.8020 (ttt) cc_final: 0.7734 (ttm) REVERT: E 35 TRP cc_start: 0.8161 (m100) cc_final: 0.7457 (m100) REVERT: E 103 GLN cc_start: 0.9231 (tp40) cc_final: 0.8776 (tm-30) REVERT: E 178 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7841 (ttp80) REVERT: E 491 ILE cc_start: 0.9089 (mm) cc_final: 0.8776 (tp) REVERT: D 534 SER cc_start: 0.9151 (p) cc_final: 0.8919 (p) REVERT: F 82 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: F 111 LEU cc_start: 0.9219 (tp) cc_final: 0.8938 (tp) REVERT: F 125 LEU cc_start: 0.8757 (tp) cc_final: 0.8201 (tp) REVERT: F 258 GLN cc_start: 0.8750 (mt0) cc_final: 0.8533 (tt0) REVERT: F 290 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8401 (mt-10) REVERT: F 426 MET cc_start: 0.7962 (mtp) cc_final: 0.7090 (mmt) outliers start: 76 outliers final: 64 residues processed: 391 average time/residue: 0.2614 time to fit residues: 153.8757 Evaluate side-chains 403 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 338 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 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 443 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 534 SER 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 618 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 641 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 622 ILE 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 110 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 138 ILE 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 365 SER Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 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 123 THR Chi-restraints excluded: chain F residue 128 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 274 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 494 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15429 Z= 0.323 Angle : 0.689 15.528 20977 Z= 0.345 Chirality : 0.049 0.371 2614 Planarity : 0.004 0.060 2601 Dihedral : 6.538 58.527 3436 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.61 % Rotamer: Outliers : 5.75 % Allowed : 19.13 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1616 helix: 1.35 (0.27), residues: 380 sheet: -0.14 (0.24), residues: 427 loop : -0.69 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 35 HIS 0.004 0.001 HIS E 375 PHE 0.015 0.002 PHE D 522 TYR 0.015 0.002 TYR E 318 ARG 0.013 0.001 ARG F 178 *********************** 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 434 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 349 time to evaluate : 1.725 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 97 LYS cc_start: 0.8966 (mptt) cc_final: 0.8350 (tptt) REVERT: A 104 MET cc_start: 0.8845 (ttm) cc_final: 0.8564 (tpp) REVERT: A 249 HIS cc_start: 0.8873 (p-80) cc_final: 0.8375 (p-80) REVERT: A 278 THR cc_start: 0.8716 (p) cc_final: 0.8157 (t) REVERT: A 474 ASP cc_start: 0.8653 (t70) cc_final: 0.7812 (p0) REVERT: B 626 MET cc_start: 0.8035 (ttt) cc_final: 0.7835 (ttm) REVERT: E 35 TRP cc_start: 0.8273 (m100) cc_final: 0.7852 (m100) REVERT: E 178 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7791 (ttp80) REVERT: E 491 ILE cc_start: 0.9078 (mm) cc_final: 0.8781 (tp) REVERT: D 534 SER cc_start: 0.9158 (p) cc_final: 0.8909 (p) REVERT: F 82 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: F 111 LEU cc_start: 0.9270 (tp) cc_final: 0.8982 (tp) REVERT: F 125 LEU cc_start: 0.8838 (tp) cc_final: 0.8291 (tp) REVERT: F 258 GLN cc_start: 0.8812 (mt0) cc_final: 0.8508 (tt0) REVERT: F 426 MET cc_start: 0.7954 (mtp) cc_final: 0.7310 (mmt) REVERT: F 432 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8357 (mm-40) outliers start: 85 outliers final: 74 residues processed: 394 average time/residue: 0.2603 time to fit residues: 153.4498 Evaluate side-chains 417 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 341 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 66 HIS 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 172 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 255 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 424 ILE 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 534 SER 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 632 ASP 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 622 ILE 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 110 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 138 ILE 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 365 SER Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 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 95 MET 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 128 THR Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15429 Z= 0.337 Angle : 0.712 15.376 20977 Z= 0.354 Chirality : 0.050 0.379 2614 Planarity : 0.004 0.061 2601 Dihedral : 6.765 59.857 3436 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 5.68 % Allowed : 20.62 % Favored : 73.70 % 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: -0.24 (0.20), residues: 1616 helix: 1.33 (0.27), residues: 373 sheet: -0.23 (0.24), residues: 424 loop : -0.79 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 35 HIS 0.004 0.001 HIS E 375 PHE 0.014 0.002 PHE D 522 TYR 0.015 0.002 TYR E 318 ARG 0.012 0.001 ARG F 178 *********************** 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 445 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 361 time to evaluate : 1.631 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 69 TRP cc_start: 0.8597 (m-90) cc_final: 0.8371 (m-90) REVERT: A 97 LYS cc_start: 0.8953 (mptt) cc_final: 0.8342 (tptp) REVERT: A 197 ASN cc_start: 0.7197 (p0) cc_final: 0.6787 (m110) REVERT: A 278 THR cc_start: 0.8730 (p) cc_final: 0.8177 (t) REVERT: A 474 ASP cc_start: 0.8696 (t70) cc_final: 0.7702 (p0) REVERT: B 540 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8697 (mp10) REVERT: B 624 ASP cc_start: 0.8613 (t70) cc_final: 0.8161 (t70) REVERT: B 626 MET cc_start: 0.8047 (ttt) cc_final: 0.7811 (ttm) REVERT: E 35 TRP cc_start: 0.8355 (m100) cc_final: 0.8015 (m100) REVERT: E 102 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7592 (tm-30) REVERT: E 491 ILE cc_start: 0.9077 (mm) cc_final: 0.8802 (tp) REVERT: D 534 SER cc_start: 0.9155 (p) cc_final: 0.8907 (p) REVERT: F 82 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: F 111 LEU cc_start: 0.9293 (tp) cc_final: 0.8970 (tp) REVERT: F 125 LEU cc_start: 0.8862 (tp) cc_final: 0.8343 (tp) REVERT: F 258 GLN cc_start: 0.8836 (mt0) cc_final: 0.8512 (tt0) REVERT: F 290 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8385 (mt-10) REVERT: F 426 MET cc_start: 0.7878 (mtp) cc_final: 0.7218 (mmt) REVERT: F 432 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8360 (mm-40) outliers start: 84 outliers final: 74 residues processed: 406 average time/residue: 0.2519 time to fit residues: 154.5951 Evaluate side-chains 425 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 348 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 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 172 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 255 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 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 641 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 622 ILE 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 110 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 259 LEU 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 365 SER Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 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 95 MET 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 128 THR Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 9.9990 chunk 106 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS E 195 ASN E 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15429 Z= 0.238 Angle : 0.663 14.350 20977 Z= 0.330 Chirality : 0.048 0.383 2614 Planarity : 0.004 0.061 2601 Dihedral : 6.570 58.673 3436 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 5.07 % Allowed : 21.16 % Favored : 73.77 % 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: -0.17 (0.20), residues: 1616 helix: 1.50 (0.28), residues: 373 sheet: -0.20 (0.24), residues: 419 loop : -0.79 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.006 0.001 HIS A 249 PHE 0.017 0.002 PHE F 392 TYR 0.021 0.001 TYR A 486 ARG 0.011 0.001 ARG F 178 ********************** 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 429 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 354 time to evaluate : 1.609 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 97 LYS cc_start: 0.8943 (mptt) cc_final: 0.8265 (tptp) REVERT: A 278 THR cc_start: 0.8685 (p) cc_final: 0.8123 (t) REVERT: A 474 ASP cc_start: 0.8627 (t70) cc_final: 0.7624 (p0) REVERT: B 624 ASP cc_start: 0.8701 (t70) cc_final: 0.8305 (t70) REVERT: B 626 MET cc_start: 0.8003 (ttt) cc_final: 0.7721 (ttm) REVERT: E 178 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7659 (tmm160) REVERT: E 284 ILE cc_start: 0.9246 (mt) cc_final: 0.8879 (tt) REVERT: E 491 ILE cc_start: 0.9065 (mm) cc_final: 0.8784 (tp) REVERT: D 534 SER cc_start: 0.9139 (p) cc_final: 0.8902 (p) REVERT: F 82 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: F 111 LEU cc_start: 0.9231 (tp) cc_final: 0.8950 (tp) REVERT: F 125 LEU cc_start: 0.8846 (tp) cc_final: 0.8335 (tp) REVERT: F 258 GLN cc_start: 0.8730 (mt0) cc_final: 0.8523 (tt0) REVERT: F 290 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8336 (mt-10) REVERT: F 426 MET cc_start: 0.7865 (mtp) cc_final: 0.7262 (mmt) REVERT: F 432 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8346 (mm-40) outliers start: 75 outliers final: 67 residues processed: 393 average time/residue: 0.2536 time to fit residues: 150.2970 Evaluate side-chains 412 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 343 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 66 HIS 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 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 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 534 SER 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 595 ILE 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 110 SER Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 138 ILE 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 365 SER Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 394 SER 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 606 THR Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 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 82 GLN Chi-restraints excluded: chain F residue 95 MET 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 128 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 274 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain F residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 60 optimal weight: 0.0670 chunk 149 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.125405 restraints weight = 23594.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.129208 restraints weight = 12840.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131765 restraints weight = 8499.417| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15429 Z= 0.198 Angle : 0.631 14.256 20977 Z= 0.315 Chirality : 0.047 0.378 2614 Planarity : 0.004 0.060 2601 Dihedral : 6.331 57.287 3436 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 4.33 % Allowed : 21.97 % Favored : 73.70 % 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: -0.08 (0.21), residues: 1616 helix: 1.49 (0.28), residues: 380 sheet: -0.07 (0.24), residues: 418 loop : -0.75 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 339 HIS 0.005 0.001 HIS F 375 PHE 0.016 0.001 PHE F 392 TYR 0.016 0.001 TYR A 486 ARG 0.011 0.001 ARG F 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3526.01 seconds wall clock time: 65 minutes 13.33 seconds (3913.33 seconds total)