Starting phenix.real_space_refine on Fri Feb 23 05:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiz_31607/02_2024/7fiz_31607_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiz_31607/02_2024/7fiz_31607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiz_31607/02_2024/7fiz_31607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiz_31607/02_2024/7fiz_31607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiz_31607/02_2024/7fiz_31607_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fiz_31607/02_2024/7fiz_31607_updated.pdb" } resolution = 3.28 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= 0.001 sd= 0.100 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 136 5.16 5 C 23318 2.51 5 N 6485 2.21 5 O 7017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 386": "OD1" <-> "OD2" Residue "B ASP 675": "OD1" <-> "OD2" Residue "F TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 675": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36970 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "E" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "F" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 727} Chain: "A" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "S" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 111 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.31, per 1000 atoms: 0.50 Number of scatterers: 36970 At special positions: 0 Unit cell: (206.64, 205.82, 186.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 14 15.00 O 7017 8.00 N 6485 7.00 C 23318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 13.33 Conformation dependent library (CDL) restraints added in 6.3 seconds 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 32 sheets defined 39.6% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.60 Creating SS restraints... Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 118 through 137 Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 185 through 237 Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 260 through 274 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 310 through 318 removed outlier: 3.796A pdb=" N GLU B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 removed outlier: 4.220A pdb=" N ARG B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 removed outlier: 4.557A pdb=" N ARG B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 495 through 513 removed outlier: 4.898A pdb=" N TRP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.810A pdb=" N LEU B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 575 through 578 No H-bonds generated for 'chain 'B' and resid 575 through 578' Processing helix chain 'B' and resid 631 through 645 Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 748 through 751 No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 762 through 768 Processing helix chain 'C' and resid 28 through 38 removed outlier: 3.601A pdb=" N ARG C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 138 removed outlier: 3.877A pdb=" N ALA C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 150 No H-bonds generated for 'chain 'C' and resid 147 through 150' Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 185 through 235 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 260 through 275 removed outlier: 3.854A pdb=" N ARG C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 323 through 338 Processing helix chain 'C' and resid 362 through 371 removed outlier: 4.056A pdb=" N ARG C 366 " --> pdb=" O SER C 363 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 369 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.910A pdb=" N ARG C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.694A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'C' and resid 541 through 560 Processing helix chain 'C' and resid 574 through 578 Processing helix chain 'C' and resid 631 through 646 Processing helix chain 'C' and resid 648 through 651 No H-bonds generated for 'chain 'C' and resid 648 through 651' Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 750 through 753 No H-bonds generated for 'chain 'C' and resid 750 through 753' Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'D' and resid 28 through 40 removed outlier: 4.942A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 removed outlier: 3.753A pdb=" N ALA D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 180 Processing helix chain 'D' and resid 185 through 235 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.959A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.420A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 479 through 484 removed outlier: 4.534A pdb=" N ARG D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.762A pdb=" N SER D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'D' and resid 541 through 560 Processing helix chain 'D' and resid 573 through 577 Processing helix chain 'D' and resid 631 through 646 Processing helix chain 'D' and resid 680 through 691 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 737 through 739 No H-bonds generated for 'chain 'D' and resid 737 through 739' Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.935A pdb=" N GLY D 753 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 768 Processing helix chain 'E' and resid 28 through 38 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 118 through 138 Processing helix chain 'E' and resid 158 through 168 removed outlier: 3.595A pdb=" N HIS E 168 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 185 through 237 removed outlier: 3.620A pdb=" N GLU E 228 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 255 Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 281 through 294 Processing helix chain 'E' and resid 308 through 315 Processing helix chain 'E' and resid 323 through 338 Processing helix chain 'E' and resid 361 through 372 Processing helix chain 'E' and resid 387 through 389 No H-bonds generated for 'chain 'E' and resid 387 through 389' Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 435 through 441 removed outlier: 3.590A pdb=" N LEU E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 484 removed outlier: 5.319A pdb=" N ARG E 484 " --> pdb=" O PRO E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 507 through 513 Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 541 through 560 Processing helix chain 'E' and resid 571 through 574 No H-bonds generated for 'chain 'E' and resid 571 through 574' Processing helix chain 'E' and resid 631 through 645 Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 728 Processing helix chain 'E' and resid 737 through 739 No H-bonds generated for 'chain 'E' and resid 737 through 739' Processing helix chain 'E' and resid 741 through 745 removed outlier: 4.135A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU E 745 " --> pdb=" O GLN E 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 741 through 745' Processing helix chain 'E' and resid 748 through 751 No H-bonds generated for 'chain 'E' and resid 748 through 751' Processing helix chain 'E' and resid 762 through 768 Processing helix chain 'F' and resid 28 through 38 removed outlier: 4.124A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 138 removed outlier: 4.263A pdb=" N LYS F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL F 136 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 150 through 153 No H-bonds generated for 'chain 'F' and resid 150 through 153' Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 173 through 181 Processing helix chain 'F' and resid 185 through 236 removed outlier: 3.824A pdb=" N ARG F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 244 No H-bonds generated for 'chain 'F' and resid 242 through 244' Processing helix chain 'F' and resid 252 through 255 No H-bonds generated for 'chain 'F' and resid 252 through 255' Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.542A pdb=" N LYS F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 308 through 317 Processing helix chain 'F' and resid 323 through 338 removed outlier: 4.112A pdb=" N TYR F 332 " --> pdb=" O ARG F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 387 through 390 No H-bonds generated for 'chain 'F' and resid 387 through 390' Processing helix chain 'F' and resid 404 through 410 Processing helix chain 'F' and resid 437 through 443 removed outlier: 3.686A pdb=" N VAL F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 449 No H-bonds generated for 'chain 'F' and resid 447 through 449' Processing helix chain 'F' and resid 480 through 483 Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 507 through 514 removed outlier: 4.304A pdb=" N SER F 514 " --> pdb=" O GLN F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 541 through 560 Processing helix chain 'F' and resid 631 through 646 removed outlier: 3.656A pdb=" N ALA F 646 " --> pdb=" O THR F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 692 Processing helix chain 'F' and resid 718 through 728 removed outlier: 3.593A pdb=" N ALA F 728 " --> pdb=" O ALA F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 745 removed outlier: 4.284A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 751 No H-bonds generated for 'chain 'F' and resid 748 through 751' Processing helix chain 'F' and resid 762 through 766 Processing helix chain 'A' and resid 28 through 38 removed outlier: 4.342A pdb=" N ALA A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'A' and resid 147 through 150 No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 240 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 260 through 269 removed outlier: 4.182A pdb=" N GLU A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 495 through 512 Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.605A pdb=" N ILE A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.596A pdb=" N LEU A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.774A pdb=" N GLU A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY A 753 " --> pdb=" O GLU A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 753' Processing helix chain 'A' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'B' and resid 7 through 10 removed outlier: 8.715A pdb=" N ILE B 8 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE B 45 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU B 10 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 47 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 46 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 67 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET B 85 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA B 74 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLN B 83 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 25 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 86 " --> pdb=" O THR B 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 486 through 489 removed outlier: 6.583A pdb=" N PHE B 467 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B 423 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASP B 422 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 596 through 601 removed outlier: 4.012A pdb=" N VAL B 617 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.695A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 20 through 23 Processing sheet with id= F, first strand: chain 'C' and resid 43 through 45 Processing sheet with id= G, first strand: chain 'C' and resid 486 through 489 removed outlier: 3.528A pdb=" N VAL C 354 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE C 467 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LEU C 353 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C 469 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 377 " --> pdb=" O VAL C 418 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 520 through 522 removed outlier: 5.899A pdb=" N ARG C 567 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 596 through 603 removed outlier: 3.518A pdb=" N VAL C 617 " --> pdb=" O ASP C 662 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 733 through 736 Processing sheet with id= K, first strand: chain 'D' and resid 7 through 10 removed outlier: 7.746A pdb=" N ILE D 8 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE D 45 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU D 10 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL D 47 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 67 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA D 48 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N TRP D 65 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 82 " --> pdb=" O VAL D 25 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.929A pdb=" N ASP D 96 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 106 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG D 104 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 486 through 489 removed outlier: 6.733A pdb=" N PHE D 467 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU D 353 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 469 " --> pdb=" O LEU D 353 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.428A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 601 through 603 removed outlier: 3.931A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 612 through 618 removed outlier: 3.586A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP D 662 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL D 667 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR D 626 " --> pdb=" O VAL D 667 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 700 through 702 removed outlier: 6.597A pdb=" N LYS D 732 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 20 through 25 Processing sheet with id= S, first strand: chain 'E' and resid 43 through 47 removed outlier: 3.769A pdb=" N ILE E 44 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 376 through 380 removed outlier: 6.189A pdb=" N VAL E 418 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE E 379 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU E 420 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE E 466 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU E 421 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE E 468 " --> pdb=" O LEU E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 596 through 603 removed outlier: 3.658A pdb=" N THR E 603 " --> pdb=" O GLY E 606 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 606 " --> pdb=" O THR E 603 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.418A pdb=" N LYS E 732 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 20 through 23 removed outlier: 7.344A pdb=" N GLN F 68 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 67 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 486 through 489 removed outlier: 7.631A pdb=" N PHE F 467 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LEU F 353 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR F 469 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE F 419 " --> pdb=" O PHE F 466 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.579A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 596 through 601 removed outlier: 4.486A pdb=" N THR F 611 " --> pdb=" O PRO F 668 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL F 617 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 667 " --> pdb=" O THR F 626 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 732 through 736 removed outlier: 6.707A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'A' and resid 20 through 25 removed outlier: 6.176A pdb=" N GLN A 68 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG A 91 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 66 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 69 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 44 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.667A pdb=" N LEU A 351 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.578A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'A' and resid 596 through 603 removed outlier: 3.848A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 611 " --> pdb=" O PRO A 668 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 664 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 617 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 662 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS A 622 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 665 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL A 667 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N THR A 626 " --> pdb=" O VAL A 667 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.474A pdb=" N LYS A 732 " --> pdb=" O ALA A 701 " (cutoff:3.500A) 1328 hydrogen bonds defined for protein. 3912 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: 12.37 Time building geometry restraints manager: 14.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.28: 6398 1.28 - 1.44: 8905 1.44 - 1.61: 22074 1.61 - 1.78: 35 1.78 - 1.95: 233 Bond restraints: 37645 Sorted by residual: bond pdb=" C ALA F 679 " pdb=" O ALA F 679 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.19e-02 7.06e+03 1.20e+02 bond pdb=" C ASP A 675 " pdb=" O ASP A 675 " ideal model delta sigma weight residual 1.235 1.125 0.111 1.02e-02 9.61e+03 1.17e+02 bond pdb=" C ALA D 679 " pdb=" O ALA D 679 " ideal model delta sigma weight residual 1.233 1.108 0.125 1.30e-02 5.92e+03 9.27e+01 bond pdb=" C ASP E 675 " pdb=" O ASP E 675 " ideal model delta sigma weight residual 1.235 1.129 0.106 1.14e-02 7.69e+03 8.67e+01 bond pdb=" C ASP D 675 " pdb=" O ASP D 675 " ideal model delta sigma weight residual 1.234 1.123 0.111 1.20e-02 6.94e+03 8.53e+01 ... (remaining 37640 not shown) Histogram of bond angle deviations from ideal: 94.64 - 102.92: 297 102.92 - 111.20: 15070 111.20 - 119.48: 17711 119.48 - 127.76: 17649 127.76 - 136.04: 343 Bond angle restraints: 51070 Sorted by residual: angle pdb=" O ASP B 675 " pdb=" C ASP B 675 " pdb=" N GLY B 676 " ideal model delta sigma weight residual 123.42 106.29 17.13 1.07e+00 8.73e-01 2.56e+02 angle pdb=" O ASP A 675 " pdb=" C ASP A 675 " pdb=" N GLY A 676 " ideal model delta sigma weight residual 123.04 106.75 16.29 1.04e+00 9.25e-01 2.45e+02 angle pdb=" O ASP D 675 " pdb=" C ASP D 675 " pdb=" N GLY D 676 " ideal model delta sigma weight residual 123.42 107.21 16.21 1.07e+00 8.73e-01 2.30e+02 angle pdb=" O ALA F 679 " pdb=" C ALA F 679 " pdb=" N GLY F 680 " ideal model delta sigma weight residual 122.15 105.35 16.80 1.14e+00 7.69e-01 2.17e+02 angle pdb=" O ASP E 675 " pdb=" C ASP E 675 " pdb=" N GLY E 676 " ideal model delta sigma weight residual 123.31 106.58 16.73 1.17e+00 7.31e-01 2.05e+02 ... (remaining 51065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.79: 22827 27.79 - 55.58: 366 55.58 - 83.37: 63 83.37 - 111.16: 2 111.16 - 138.95: 4 Dihedral angle restraints: 23262 sinusoidal: 9703 harmonic: 13559 Sorted by residual: dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual -180.00 -99.39 -80.61 0 5.00e+00 4.00e-02 2.60e+02 dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual -180.00 -106.19 -73.81 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA GLU F 240 " pdb=" C GLU F 240 " pdb=" N ASP F 241 " pdb=" CA ASP F 241 " ideal model delta harmonic sigma weight residual 180.00 108.62 71.38 0 5.00e+00 4.00e-02 2.04e+02 ... (remaining 23259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5358 0.106 - 0.212: 452 0.212 - 0.318: 14 0.318 - 0.424: 3 0.424 - 0.530: 1 Chirality restraints: 5828 Sorted by residual: chirality pdb=" CA SER F 380 " pdb=" N SER F 380 " pdb=" C SER F 380 " pdb=" CB SER F 380 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA ARG B 385 " pdb=" N ARG B 385 " pdb=" C ARG B 385 " pdb=" CB ARG B 385 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CG LEU B 237 " pdb=" CB LEU B 237 " pdb=" CD1 LEU B 237 " pdb=" CD2 LEU B 237 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 5825 not shown) Planarity restraints: 6627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 679 " -0.091 2.00e-02 2.50e+03 1.78e-01 3.17e+02 pdb=" C ALA F 679 " 0.307 2.00e-02 2.50e+03 pdb=" O ALA F 679 " -0.130 2.00e-02 2.50e+03 pdb=" N GLY F 680 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 675 " -0.089 2.00e-02 2.50e+03 1.74e-01 3.04e+02 pdb=" C ASP B 675 " 0.300 2.00e-02 2.50e+03 pdb=" O ASP B 675 " -0.129 2.00e-02 2.50e+03 pdb=" N GLY B 676 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 679 " -0.090 2.00e-02 2.50e+03 1.74e-01 3.03e+02 pdb=" C ALA C 679 " 0.299 2.00e-02 2.50e+03 pdb=" O ALA C 679 " -0.132 2.00e-02 2.50e+03 pdb=" N GLY C 680 " -0.077 2.00e-02 2.50e+03 ... (remaining 6624 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4413 2.75 - 3.29: 34653 3.29 - 3.82: 60367 3.82 - 4.36: 70696 4.36 - 4.90: 119744 Nonbonded interactions: 289873 Sorted by model distance: nonbonded pdb=" OH TYR A 135 " pdb=" OD2 ASP A 199 " model vdw 2.212 2.440 nonbonded pdb=" O GLN F 278 " pdb=" OG SER F 280 " model vdw 2.221 2.440 nonbonded pdb=" O ASP B 422 " pdb=" OG1 THR B 470 " model vdw 2.229 2.440 nonbonded pdb=" O GLN D 234 " pdb=" OG SER D 244 " model vdw 2.230 2.440 nonbonded pdb=" O VAL B 359 " pdb=" O2B AGS B 901 " model vdw 2.257 2.440 ... (remaining 289868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 780) selection = (chain 'B' and resid 2 through 780) selection = (chain 'C' and resid 2 through 780) selection = (chain 'D' and resid 2 through 780) selection = chain 'E' selection = (chain 'F' and resid 2 through 780) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 10.090 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 89.010 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 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 : 0.008 0.130 37645 Z= 0.542 Angle : 1.139 17.129 51070 Z= 0.664 Chirality : 0.060 0.530 5828 Planarity : 0.011 0.178 6627 Dihedral : 11.032 138.949 14530 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.93 % Favored : 92.86 % Rotamer: Outliers : 0.31 % Allowed : 3.23 % Favored : 96.46 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.25 % 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: -4.01 (0.10), residues: 4662 helix: -2.39 (0.09), residues: 1949 sheet: -2.52 (0.19), residues: 610 loop : -2.88 (0.11), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP F 292 HIS 0.014 0.002 HIS D 454 PHE 0.033 0.003 PHE C 45 TYR 0.048 0.003 TYR B 225 ARG 0.014 0.001 ARG F 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 568 time to evaluate : 4.530 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: B 308 ILE cc_start: 0.8689 (pt) cc_final: 0.8486 (mp) REVERT: B 344 VAL cc_start: 0.9324 (m) cc_final: 0.8972 (t) REVERT: B 385 ARG cc_start: 0.8248 (ptt180) cc_final: 0.7812 (ptt90) REVERT: B 401 MET cc_start: 0.8315 (tpp) cc_final: 0.8058 (ttp) REVERT: B 612 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 282 GLU cc_start: 0.8326 (pt0) cc_final: 0.7950 (tp30) REVERT: C 432 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6271 (ttm110) REVERT: D 276 MET cc_start: 0.7886 (ptm) cc_final: 0.7540 (ptt) REVERT: D 423 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 626 THR cc_start: 0.7506 (p) cc_final: 0.7185 (p) REVERT: E 351 LEU cc_start: 0.6890 (mt) cc_final: 0.6467 (mt) REVERT: E 387 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7993 (mp0) REVERT: E 466 PHE cc_start: 0.8032 (t80) cc_final: 0.7815 (t80) REVERT: E 485 MET cc_start: 0.8329 (mtt) cc_final: 0.8127 (mtt) REVERT: E 486 GLU cc_start: 0.7392 (tt0) cc_final: 0.6493 (tt0) REVERT: F 420 LEU cc_start: 0.7656 (tt) cc_final: 0.6952 (tp) REVERT: F 431 TRP cc_start: 0.6536 (p90) cc_final: 0.6324 (p-90) REVERT: F 456 LEU cc_start: 0.8019 (tp) cc_final: 0.7768 (tp) REVERT: F 516 MET cc_start: 0.8008 (mmm) cc_final: 0.7797 (mmm) REVERT: A 336 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8269 (mtt90) REVERT: A 401 MET cc_start: 0.7051 (tpt) cc_final: 0.6070 (tmm) REVERT: A 423 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7966 (mp0) REVERT: A 424 ILE cc_start: 0.8888 (pt) cc_final: 0.8640 (mt) REVERT: A 440 LEU cc_start: 0.8120 (tp) cc_final: 0.7880 (tp) REVERT: A 477 ILE cc_start: 0.8318 (mt) cc_final: 0.8010 (mp) outliers start: 12 outliers final: 4 residues processed: 577 average time/residue: 0.5754 time to fit residues: 507.9051 Evaluate side-chains 318 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 312 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 432 ARG Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain A residue 243 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 30.0000 chunk 351 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 237 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 421 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN B 411 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN C 177 GLN C 211 GLN C 221 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 731 HIS D 138 ASN D 407 HIS D 666 HIS E 49 GLN E 138 ASN E 216 GLN E 220 ASN E 234 GLN E 510 GLN E 649 GLN E 727 GLN F 220 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN F 647 HIS ** F 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 ASN A 138 ASN A 139 HIS A 177 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN A 647 HIS A 666 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37645 Z= 0.278 Angle : 0.701 22.776 51070 Z= 0.351 Chirality : 0.045 0.168 5828 Planarity : 0.006 0.086 6627 Dihedral : 8.470 139.010 5269 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.08 % Rotamer: Outliers : 1.98 % Allowed : 7.40 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.09 % 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: -2.70 (0.11), residues: 4662 helix: -0.86 (0.11), residues: 1970 sheet: -2.15 (0.19), residues: 624 loop : -2.57 (0.12), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 507 HIS 0.007 0.001 HIS D 454 PHE 0.012 0.001 PHE C 45 TYR 0.025 0.002 TYR C 224 ARG 0.008 0.001 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 324 time to evaluate : 4.311 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: B 308 ILE cc_start: 0.8687 (pt) cc_final: 0.8458 (mp) REVERT: B 343 ASP cc_start: 0.7529 (t70) cc_final: 0.7272 (t0) REVERT: B 385 ARG cc_start: 0.8178 (ptt180) cc_final: 0.7945 (ptm-80) REVERT: B 401 MET cc_start: 0.8402 (tpp) cc_final: 0.8085 (mtm) REVERT: C 75 MET cc_start: 0.4044 (mtp) cc_final: 0.3703 (mtp) REVERT: C 282 GLU cc_start: 0.8546 (pt0) cc_final: 0.8020 (tp30) REVERT: D 180 LEU cc_start: 0.1588 (OUTLIER) cc_final: 0.1151 (pt) REVERT: D 423 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8119 (mm-30) REVERT: D 512 ARG cc_start: 0.7460 (tmm160) cc_final: 0.7229 (ttp80) REVERT: F 217 MET cc_start: 0.1206 (tpt) cc_final: 0.0458 (ptm) REVERT: F 276 MET cc_start: 0.3904 (OUTLIER) cc_final: 0.3349 (pmm) REVERT: F 420 LEU cc_start: 0.7473 (tt) cc_final: 0.7202 (tt) REVERT: F 516 MET cc_start: 0.8118 (mmm) cc_final: 0.7596 (mmm) REVERT: F 698 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6637 (mpp) REVERT: A 160 MET cc_start: 0.0750 (ptm) cc_final: 0.0097 (ptp) REVERT: A 336 ARG cc_start: 0.8710 (mtt180) cc_final: 0.8367 (mtm180) REVERT: A 401 MET cc_start: 0.7250 (tpt) cc_final: 0.6250 (tmm) REVERT: A 423 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7871 (mp0) outliers start: 78 outliers final: 37 residues processed: 383 average time/residue: 0.5262 time to fit residues: 322.7911 Evaluate side-chains 300 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 698 MET Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 40.0000 chunk 130 optimal weight: 8.9990 chunk 350 optimal weight: 0.5980 chunk 286 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 422 optimal weight: 8.9990 chunk 456 optimal weight: 7.9990 chunk 375 optimal weight: 0.0270 chunk 418 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 338 optimal weight: 8.9990 overall best weight: 2.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS C 221 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS D 407 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 220 ASN E 319 HIS ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 HIS ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 ASN A 416 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37645 Z= 0.203 Angle : 0.627 23.319 51070 Z= 0.309 Chirality : 0.043 0.209 5828 Planarity : 0.005 0.076 6627 Dihedral : 7.730 137.736 5259 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.38 % Favored : 94.51 % Rotamer: Outliers : 2.04 % Allowed : 9.13 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % 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: -1.91 (0.12), residues: 4662 helix: -0.03 (0.11), residues: 1991 sheet: -1.91 (0.19), residues: 638 loop : -2.31 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 602 HIS 0.006 0.001 HIS D 454 PHE 0.025 0.001 PHE E 466 TYR 0.022 0.001 TYR B 332 ARG 0.020 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 298 time to evaluate : 4.586 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: B 308 ILE cc_start: 0.8610 (pt) cc_final: 0.8381 (mp) REVERT: B 343 ASP cc_start: 0.7534 (t70) cc_final: 0.7178 (t0) REVERT: B 385 ARG cc_start: 0.8176 (ptt180) cc_final: 0.7904 (ptm-80) REVERT: B 401 MET cc_start: 0.8384 (tpp) cc_final: 0.8114 (mtm) REVERT: C 75 MET cc_start: 0.3852 (mtp) cc_final: 0.3584 (mtp) REVERT: C 282 GLU cc_start: 0.8544 (pt0) cc_final: 0.7973 (tp30) REVERT: C 385 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7161 (tpp80) REVERT: D 423 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 401 MET cc_start: 0.6890 (mmm) cc_final: 0.6535 (mmm) REVERT: E 407 HIS cc_start: 0.8890 (m90) cc_final: 0.8629 (m90) REVERT: E 674 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.4739 (mtmm) REVERT: F 516 MET cc_start: 0.8140 (mmm) cc_final: 0.7657 (mmm) REVERT: F 531 ILE cc_start: 0.8373 (mt) cc_final: 0.8100 (mm) REVERT: F 698 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6843 (mpp) REVERT: A 160 MET cc_start: 0.0659 (ptm) cc_final: -0.0021 (ptp) REVERT: A 336 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8333 (mtm180) REVERT: A 352 VAL cc_start: 0.8880 (t) cc_final: 0.8588 (p) REVERT: A 401 MET cc_start: 0.7328 (tpt) cc_final: 0.6241 (tmm) REVERT: A 423 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7671 (mm-30) REVERT: A 487 VAL cc_start: 0.9228 (m) cc_final: 0.8935 (t) outliers start: 80 outliers final: 47 residues processed: 352 average time/residue: 0.5064 time to fit residues: 291.7489 Evaluate side-chains 312 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 263 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 633 MET Chi-restraints excluded: chain E residue 674 LYS Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 574 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 698 MET Chi-restraints excluded: chain F residue 699 ASP Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 373 ASN Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 423 optimal weight: 8.9990 chunk 448 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 401 optimal weight: 40.0000 chunk 120 optimal weight: 0.6980 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN E 628 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37645 Z= 0.307 Angle : 0.658 22.489 51070 Z= 0.326 Chirality : 0.044 0.170 5828 Planarity : 0.005 0.069 6627 Dihedral : 7.626 137.411 5259 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.37 % Favored : 93.52 % Rotamer: Outliers : 2.82 % Allowed : 9.90 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % 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: -1.68 (0.12), residues: 4662 helix: 0.20 (0.12), residues: 2000 sheet: -1.75 (0.19), residues: 609 loop : -2.25 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 298 HIS 0.010 0.001 HIS D 664 PHE 0.013 0.001 PHE E 467 TYR 0.022 0.002 TYR B 332 ARG 0.011 0.001 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 269 time to evaluate : 4.059 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: B 308 ILE cc_start: 0.8576 (pt) cc_final: 0.8282 (mp) REVERT: B 343 ASP cc_start: 0.7528 (t70) cc_final: 0.7177 (t0) REVERT: B 385 ARG cc_start: 0.8213 (ptt180) cc_final: 0.7929 (ttp80) REVERT: B 401 MET cc_start: 0.8389 (tpp) cc_final: 0.8129 (mtm) REVERT: C 282 GLU cc_start: 0.8600 (pt0) cc_final: 0.7994 (tp30) REVERT: C 385 ARG cc_start: 0.7641 (tpp80) cc_final: 0.7144 (tpp80) REVERT: D 180 LEU cc_start: 0.1467 (OUTLIER) cc_final: 0.1093 (pt) REVERT: D 423 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8361 (mm-30) REVERT: E 217 MET cc_start: 0.4733 (mmp) cc_final: 0.4472 (mmt) REVERT: E 401 MET cc_start: 0.6990 (mmm) cc_final: 0.6623 (mmm) REVERT: E 407 HIS cc_start: 0.8863 (m90) cc_final: 0.8621 (m90) REVERT: E 516 MET cc_start: 0.7058 (tpp) cc_final: 0.6789 (tpp) REVERT: F 217 MET cc_start: 0.1192 (tpt) cc_final: 0.0410 (ptt) REVERT: F 227 ARG cc_start: 0.4098 (mmt180) cc_final: 0.3878 (mmt180) REVERT: F 276 MET cc_start: 0.4031 (pmm) cc_final: 0.3764 (pmm) REVERT: F 482 LEU cc_start: 0.7813 (mt) cc_final: 0.7179 (mp) REVERT: F 516 MET cc_start: 0.8203 (mmm) cc_final: 0.7763 (mmm) REVERT: A 160 MET cc_start: 0.0656 (ptm) cc_final: -0.0055 (ptp) REVERT: A 336 ARG cc_start: 0.8681 (mtt180) cc_final: 0.8224 (mtm180) REVERT: A 352 VAL cc_start: 0.8908 (t) cc_final: 0.8659 (p) REVERT: A 401 MET cc_start: 0.7404 (tpt) cc_final: 0.6249 (tmm) REVERT: A 423 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 487 VAL cc_start: 0.9201 (m) cc_final: 0.8897 (t) outliers start: 111 outliers final: 73 residues processed: 346 average time/residue: 0.4835 time to fit residues: 275.7242 Evaluate side-chains 336 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 262 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 633 MET Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 698 MET Chi-restraints excluded: chain F residue 699 ASP Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 0.9990 chunk 254 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 333 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 382 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 0 optimal weight: 70.0000 chunk 229 optimal weight: 8.9990 chunk 402 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 HIS B 411 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS E 220 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 277 GLN A 416 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 37645 Z= 0.328 Angle : 0.671 20.214 51070 Z= 0.333 Chirality : 0.045 0.164 5828 Planarity : 0.005 0.067 6627 Dihedral : 7.519 136.923 5255 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.86 % Favored : 93.05 % Rotamer: Outliers : 2.93 % Allowed : 11.02 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % 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: -1.52 (0.12), residues: 4662 helix: 0.30 (0.11), residues: 2021 sheet: -1.63 (0.20), residues: 609 loop : -2.17 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 431 HIS 0.009 0.001 HIS D 664 PHE 0.019 0.002 PHE F 467 TYR 0.024 0.002 TYR B 332 ARG 0.008 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 263 time to evaluate : 3.987 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: B 251 LYS cc_start: 0.9385 (ttmt) cc_final: 0.9164 (tppt) REVERT: B 308 ILE cc_start: 0.8518 (pt) cc_final: 0.8188 (mp) REVERT: B 343 ASP cc_start: 0.7582 (t70) cc_final: 0.7180 (t0) REVERT: B 385 ARG cc_start: 0.8220 (ptt180) cc_final: 0.7911 (ttp80) REVERT: B 401 MET cc_start: 0.8504 (tpp) cc_final: 0.8299 (mtm) REVERT: C 282 GLU cc_start: 0.8603 (pt0) cc_final: 0.8006 (tp30) REVERT: C 287 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8005 (tpt-90) REVERT: D 180 LEU cc_start: 0.1560 (OUTLIER) cc_final: 0.1199 (pt) REVERT: D 423 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8386 (mm-30) REVERT: D 698 MET cc_start: 0.7932 (tpp) cc_final: 0.7515 (tpp) REVERT: E 320 TYR cc_start: 0.7353 (m-80) cc_final: 0.7119 (m-80) REVERT: E 407 HIS cc_start: 0.8875 (m90) cc_final: 0.8650 (m90) REVERT: E 516 MET cc_start: 0.7011 (tpp) cc_final: 0.6769 (tpp) REVERT: F 401 MET cc_start: 0.6775 (ptt) cc_final: 0.6287 (ptt) REVERT: F 516 MET cc_start: 0.8139 (mmm) cc_final: 0.7678 (mmm) REVERT: A 38 MET cc_start: -0.0770 (tpp) cc_final: -0.1070 (ttm) REVERT: A 160 MET cc_start: 0.0742 (ptm) cc_final: 0.0147 (ptp) REVERT: A 336 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8019 (mtm-85) REVERT: A 352 VAL cc_start: 0.8930 (t) cc_final: 0.8706 (p) REVERT: A 401 MET cc_start: 0.7487 (tpt) cc_final: 0.5855 (tmm) REVERT: A 423 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 487 VAL cc_start: 0.9251 (m) cc_final: 0.8989 (t) outliers start: 115 outliers final: 83 residues processed: 342 average time/residue: 0.4685 time to fit residues: 265.5974 Evaluate side-chains 338 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 253 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 699 ASP Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 7.9990 chunk 403 optimal weight: 30.0000 chunk 88 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 448 optimal weight: 6.9990 chunk 372 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 235 optimal weight: 40.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37645 Z= 0.318 Angle : 0.652 19.729 51070 Z= 0.324 Chirality : 0.044 0.159 5828 Planarity : 0.005 0.065 6627 Dihedral : 7.386 135.959 5255 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.99 % Rotamer: Outliers : 2.85 % Allowed : 11.45 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % 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: -1.38 (0.12), residues: 4662 helix: 0.40 (0.11), residues: 2022 sheet: -1.51 (0.20), residues: 614 loop : -2.09 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 602 HIS 0.007 0.001 HIS D 664 PHE 0.013 0.001 PHE F 467 TYR 0.022 0.002 TYR B 332 ARG 0.005 0.001 ARG F 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 260 time to evaluate : 3.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 LYS cc_start: 0.9413 (ttmt) cc_final: 0.9178 (tppt) REVERT: B 385 ARG cc_start: 0.8194 (ptt180) cc_final: 0.7903 (ttp80) REVERT: C 282 GLU cc_start: 0.8617 (pt0) cc_final: 0.8118 (tp30) REVERT: C 287 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8000 (tpt-90) REVERT: D 180 LEU cc_start: 0.1516 (OUTLIER) cc_final: 0.1132 (pt) REVERT: D 278 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7549 (mm-40) REVERT: D 423 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8322 (mm-30) REVERT: D 698 MET cc_start: 0.7912 (tpp) cc_final: 0.7420 (tpp) REVERT: E 217 MET cc_start: 0.4839 (mmp) cc_final: 0.4624 (mmt) REVERT: E 407 HIS cc_start: 0.8843 (m90) cc_final: 0.8620 (m90) REVERT: E 516 MET cc_start: 0.7015 (tpp) cc_final: 0.6751 (tpp) REVERT: F 401 MET cc_start: 0.6799 (ptt) cc_final: 0.6543 (ptt) REVERT: F 516 MET cc_start: 0.8147 (mmm) cc_final: 0.7732 (mmp) REVERT: A 160 MET cc_start: 0.0729 (ptm) cc_final: 0.0132 (ptp) REVERT: A 336 ARG cc_start: 0.8620 (mtt180) cc_final: 0.8027 (mtm-85) REVERT: A 352 VAL cc_start: 0.8921 (t) cc_final: 0.8697 (p) REVERT: A 423 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7266 (mm-30) REVERT: A 487 VAL cc_start: 0.9245 (m) cc_final: 0.8990 (t) REVERT: A 516 MET cc_start: 0.8312 (mmm) cc_final: 0.8097 (mtp) outliers start: 112 outliers final: 85 residues processed: 338 average time/residue: 0.4726 time to fit residues: 265.8561 Evaluate side-chains 333 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 246 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 699 ASP Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 327 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 chunk 377 optimal weight: 0.9990 chunk 250 optimal weight: 50.0000 chunk 447 optimal weight: 0.0040 chunk 279 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 37645 Z= 0.340 Angle : 0.671 19.581 51070 Z= 0.333 Chirality : 0.045 0.201 5828 Planarity : 0.005 0.061 6627 Dihedral : 7.355 133.836 5255 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 3.21 % Allowed : 11.86 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.07 % 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: -1.28 (0.12), residues: 4662 helix: 0.46 (0.12), residues: 2009 sheet: -1.45 (0.20), residues: 614 loop : -2.00 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 431 HIS 0.010 0.001 HIS E 18 PHE 0.018 0.002 PHE F 467 TYR 0.022 0.002 TYR C 225 ARG 0.007 0.001 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 249 time to evaluate : 4.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 LYS cc_start: 0.9410 (ttmt) cc_final: 0.9168 (tppt) REVERT: B 385 ARG cc_start: 0.8197 (ptt180) cc_final: 0.7889 (ttp80) REVERT: C 282 GLU cc_start: 0.8591 (pt0) cc_final: 0.8115 (tp30) REVERT: C 287 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7996 (tpt-90) REVERT: D 180 LEU cc_start: 0.1530 (OUTLIER) cc_final: 0.1179 (pt) REVERT: D 276 MET cc_start: 0.7867 (ptm) cc_final: 0.7647 (ptt) REVERT: D 278 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7515 (mm-40) REVERT: D 423 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8052 (mm-30) REVERT: E 38 MET cc_start: 0.4021 (mtt) cc_final: 0.2489 (ptm) REVERT: E 237 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6492 (tt) REVERT: E 516 MET cc_start: 0.7028 (tpp) cc_final: 0.6764 (tpp) REVERT: F 401 MET cc_start: 0.6902 (ptt) cc_final: 0.6572 (ptp) REVERT: F 427 MET cc_start: 0.8278 (mmt) cc_final: 0.7835 (mmm) REVERT: F 516 MET cc_start: 0.8148 (mmm) cc_final: 0.7841 (mmp) REVERT: A 160 MET cc_start: 0.0586 (ptm) cc_final: 0.0194 (ptm) REVERT: A 302 ASP cc_start: 0.7767 (m-30) cc_final: 0.7101 (p0) REVERT: A 336 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8020 (mtm-85) REVERT: A 352 VAL cc_start: 0.8918 (t) cc_final: 0.8701 (p) REVERT: A 487 VAL cc_start: 0.9241 (m) cc_final: 0.8992 (t) REVERT: A 516 MET cc_start: 0.8414 (mmm) cc_final: 0.7962 (mtp) outliers start: 126 outliers final: 96 residues processed: 338 average time/residue: 0.4602 time to fit residues: 261.3592 Evaluate side-chains 340 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 241 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 738 ASP Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 425 ASP Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 699 ASP Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 87 optimal weight: 40.0000 chunk 86 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 351 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 37645 Z= 0.443 Angle : 0.758 18.769 51070 Z= 0.377 Chirality : 0.047 0.171 5828 Planarity : 0.006 0.062 6627 Dihedral : 7.585 129.801 5255 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.52 % Favored : 91.36 % Rotamer: Outliers : 3.26 % Allowed : 12.52 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.46 % Twisted Proline : 1.45 % Twisted General : 0.09 % 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: -1.56 (0.12), residues: 4662 helix: 0.18 (0.11), residues: 2003 sheet: -1.56 (0.20), residues: 603 loop : -2.09 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 431 HIS 0.009 0.001 HIS D 664 PHE 0.025 0.002 PHE E 467 TYR 0.023 0.002 TYR C 225 ARG 0.019 0.001 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 245 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 LYS cc_start: 0.9402 (ttmt) cc_final: 0.9170 (tppt) REVERT: B 385 ARG cc_start: 0.8222 (ptt180) cc_final: 0.7876 (ttp80) REVERT: C 282 GLU cc_start: 0.8619 (pt0) cc_final: 0.8118 (tp30) REVERT: C 287 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8326 (tpt-90) REVERT: C 537 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8064 (pt0) REVERT: C 776 MET cc_start: 0.5689 (ptp) cc_final: 0.5280 (tmm) REVERT: D 180 LEU cc_start: 0.1580 (OUTLIER) cc_final: 0.1235 (pt) REVERT: D 217 MET cc_start: 0.2026 (tmm) cc_final: 0.0952 (pmm) REVERT: D 423 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8072 (mm-30) REVERT: E 237 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6513 (tt) REVERT: E 401 MET cc_start: 0.6908 (mmm) cc_final: 0.6556 (mmm) REVERT: E 516 MET cc_start: 0.6956 (tpp) cc_final: 0.6700 (tpp) REVERT: F 401 MET cc_start: 0.6955 (ptt) cc_final: 0.6628 (ptp) REVERT: F 516 MET cc_start: 0.8139 (mmm) cc_final: 0.7875 (mmp) REVERT: A 160 MET cc_start: 0.0802 (ptm) cc_final: 0.0407 (ptm) REVERT: A 302 ASP cc_start: 0.8093 (m-30) cc_final: 0.7147 (p0) REVERT: A 336 ARG cc_start: 0.8556 (mtt180) cc_final: 0.8167 (mtm-85) REVERT: A 516 MET cc_start: 0.8374 (mmm) cc_final: 0.7916 (mtp) outliers start: 128 outliers final: 105 residues processed: 340 average time/residue: 0.4821 time to fit residues: 276.5635 Evaluate side-chains 346 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 237 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 633 MET Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 738 ASP Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 699 ASP Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 9.9990 chunk 428 optimal weight: 5.9990 chunk 390 optimal weight: 0.0970 chunk 416 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 327 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 376 optimal weight: 5.9990 chunk 394 optimal weight: 30.0000 chunk 415 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37645 Z= 0.284 Angle : 0.659 18.956 51070 Z= 0.324 Chirality : 0.044 0.168 5828 Planarity : 0.005 0.072 6627 Dihedral : 7.246 126.738 5255 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.41 % Rotamer: Outliers : 2.77 % Allowed : 13.31 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.05 % 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: -1.23 (0.12), residues: 4662 helix: 0.50 (0.12), residues: 1999 sheet: -1.43 (0.20), residues: 609 loop : -1.97 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 431 HIS 0.006 0.001 HIS D 664 PHE 0.020 0.001 PHE E 657 TYR 0.022 0.001 TYR B 332 ARG 0.006 0.000 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 251 time to evaluate : 4.126 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: B 251 LYS cc_start: 0.9365 (ttmt) cc_final: 0.9130 (tppt) REVERT: B 385 ARG cc_start: 0.8148 (ptt180) cc_final: 0.7856 (ttp80) REVERT: C 287 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8012 (tpt-90) REVERT: C 776 MET cc_start: 0.5615 (ptp) cc_final: 0.5286 (tmm) REVERT: D 180 LEU cc_start: 0.1549 (OUTLIER) cc_final: 0.1220 (pt) REVERT: D 217 MET cc_start: 0.1938 (tmm) cc_final: 0.0906 (pmm) REVERT: D 423 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8071 (mm-30) REVERT: D 527 ILE cc_start: 0.7830 (mt) cc_final: 0.7410 (mm) REVERT: E 401 MET cc_start: 0.6898 (mmm) cc_final: 0.6533 (mmm) REVERT: E 482 LEU cc_start: 0.7311 (tp) cc_final: 0.7110 (tp) REVERT: E 516 MET cc_start: 0.6985 (tpp) cc_final: 0.6710 (tpp) REVERT: F 75 MET cc_start: 0.0814 (tmm) cc_final: 0.0373 (ttm) REVERT: F 347 LYS cc_start: 0.3302 (pttp) cc_final: 0.2724 (mtmt) REVERT: F 401 MET cc_start: 0.6953 (ptt) cc_final: 0.6600 (ptp) REVERT: F 516 MET cc_start: 0.8114 (mmm) cc_final: 0.7829 (mmp) REVERT: A 160 MET cc_start: 0.0597 (ptm) cc_final: 0.0197 (ptm) REVERT: A 302 ASP cc_start: 0.8046 (m-30) cc_final: 0.7156 (p0) REVERT: A 516 MET cc_start: 0.8360 (mmm) cc_final: 0.8005 (mtp) outliers start: 109 outliers final: 90 residues processed: 328 average time/residue: 0.4571 time to fit residues: 253.7827 Evaluate side-chains 337 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 245 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 776 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 699 ASP Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 3.9990 chunk 440 optimal weight: 0.7980 chunk 268 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 306 optimal weight: 0.0170 chunk 462 optimal weight: 20.0000 chunk 425 optimal weight: 4.9990 chunk 368 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN C 49 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37645 Z= 0.165 Angle : 0.599 17.397 51070 Z= 0.292 Chirality : 0.042 0.186 5828 Planarity : 0.004 0.073 6627 Dihedral : 6.734 119.658 5255 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.72 % Rotamer: Outliers : 1.83 % Allowed : 14.45 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.05 % 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 (0.13), residues: 4662 helix: 0.92 (0.12), residues: 2003 sheet: -1.20 (0.21), residues: 586 loop : -1.80 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 431 HIS 0.004 0.001 HIS E 393 PHE 0.021 0.001 PHE E 657 TYR 0.028 0.001 TYR E 225 ARG 0.005 0.000 ARG E 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 279 time to evaluate : 4.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 LYS cc_start: 0.9354 (ttmt) cc_final: 0.9119 (tppt) REVERT: B 332 TYR cc_start: 0.7171 (m-80) cc_final: 0.6938 (m-80) REVERT: B 394 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7362 (pmm150) REVERT: C 287 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7999 (tpt-90) REVERT: D 180 LEU cc_start: 0.1528 (OUTLIER) cc_final: 0.1207 (pt) REVERT: D 423 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8040 (mm-30) REVERT: D 527 ILE cc_start: 0.7818 (mt) cc_final: 0.7407 (mm) REVERT: E 401 MET cc_start: 0.6833 (mmm) cc_final: 0.6479 (mmm) REVERT: E 407 HIS cc_start: 0.7804 (m170) cc_final: 0.7595 (m90) REVERT: E 482 LEU cc_start: 0.7336 (tp) cc_final: 0.7103 (tp) REVERT: E 516 MET cc_start: 0.6936 (tpp) cc_final: 0.6712 (tpp) REVERT: E 735 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8261 (mp) REVERT: F 75 MET cc_start: 0.0612 (tmm) cc_final: 0.0171 (ttm) REVERT: F 217 MET cc_start: 0.0667 (tpt) cc_final: 0.0420 (ptt) REVERT: F 347 LYS cc_start: 0.3074 (pttp) cc_final: 0.2579 (mtmt) REVERT: F 401 MET cc_start: 0.6914 (ptt) cc_final: 0.6562 (ptp) REVERT: F 427 MET cc_start: 0.8264 (mmm) cc_final: 0.7300 (mmm) REVERT: F 513 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8447 (mm-30) REVERT: F 516 MET cc_start: 0.8136 (mmm) cc_final: 0.7858 (mmp) REVERT: F 744 GLU cc_start: 0.8113 (pp20) cc_final: 0.7866 (pp20) REVERT: A 160 MET cc_start: 0.0465 (ptm) cc_final: 0.0007 (ptm) REVERT: A 302 ASP cc_start: 0.7928 (m-30) cc_final: 0.7251 (p0) REVERT: A 516 MET cc_start: 0.8238 (mmm) cc_final: 0.8033 (mtp) outliers start: 72 outliers final: 57 residues processed: 329 average time/residue: 0.4804 time to fit residues: 261.8936 Evaluate side-chains 312 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 251 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 602 TRP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 550 ILE Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 760 GLU Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 699 ASP Chi-restraints excluded: chain F residue 746 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 779 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 6.9990 chunk 392 optimal weight: 0.5980 chunk 112 optimal weight: 0.1980 chunk 339 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 368 optimal weight: 4.9990 chunk 154 optimal weight: 40.0000 chunk 378 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN E 313 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.172779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.128442 restraints weight = 115600.556| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 5.57 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37645 Z= 0.243 Angle : 0.636 17.112 51070 Z= 0.311 Chirality : 0.043 0.176 5828 Planarity : 0.005 0.074 6627 Dihedral : 6.723 115.948 5255 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.67 % Rotamer: Outliers : 1.86 % Allowed : 14.81 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.45 % Twisted General : 0.05 % 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 (0.13), residues: 4662 helix: 0.90 (0.12), residues: 2013 sheet: -1.13 (0.21), residues: 590 loop : -1.80 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 431 HIS 0.005 0.001 HIS D 664 PHE 0.022 0.001 PHE E 657 TYR 0.031 0.001 TYR E 225 ARG 0.015 0.000 ARG E 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8374.31 seconds wall clock time: 152 minutes 5.72 seconds (9125.72 seconds total)