Starting phenix.real_space_refine on Sat Mar 23 09:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/03_2024/7ypi_34001_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/03_2024/7ypi_34001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/03_2024/7ypi_34001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/03_2024/7ypi_34001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/03_2024/7ypi_34001_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypi_34001/03_2024/7ypi_34001_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 6 5.49 5 S 128 5.16 5 C 23012 2.51 5 N 6412 2.21 5 O 6918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 222": "NH1" <-> "NH2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C ASP 570": "OD1" <-> "OD2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E ARG 212": "NH1" <-> "NH2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E GLU 486": "OE1" <-> "OE2" Residue "E TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F GLU 295": "OE1" <-> "OE2" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36476 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" 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: 18.08, per 1000 atoms: 0.50 Number of scatterers: 36476 At special positions: 0 Unit cell: (189.24, 177.62, 186.75, 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 128 16.00 P 6 15.00 O 6918 8.00 N 6412 7.00 C 23012 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: 14.02 Conformation dependent library (CDL) restraints added in 6.7 seconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 37 sheets defined 39.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.60 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' 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 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.035A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 234 removed outlier: 3.639A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.765A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.601A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.006A pdb=" N ASN A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 572 through 577 Proline residue: A 575 - end of helix No H-bonds generated for 'chain 'A' and resid 572 through 577' Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.899A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 762 through 768 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 119 through 136 Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.201A pdb=" N SER B 141 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.682A pdb=" N VAL B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 185 through 232 removed outlier: 3.668A pdb=" N THR B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.567A pdb=" N MET B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 631 through 647 removed outlier: 3.567A pdb=" N HIS B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.511A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 185 through 236 removed outlier: 4.182A pdb=" N LYS C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 removed outlier: 3.996A pdb=" N LYS C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.556A pdb=" N ASP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.858A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 371 Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 495 through 505 Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 542 through 559 Processing helix chain 'C' and resid 572 through 576 removed outlier: 3.583A pdb=" N THR C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 572 through 576' Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 742 through 744 No H-bonds generated for 'chain 'C' and resid 742 through 744' Processing helix chain 'C' and resid 748 through 751 No H-bonds generated for 'chain 'C' and resid 748 through 751' Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'D' and resid 28 through 37 removed outlier: 4.086A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 185 through 232 Processing helix chain 'D' and resid 241 through 244 No H-bonds generated for 'chain 'D' and resid 241 through 244' Processing helix chain 'D' and resid 246 through 254 Processing helix chain 'D' and resid 260 through 271 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 308 through 318 removed outlier: 4.042A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 361 through 371 Processing helix chain 'D' and resid 387 through 390 No H-bonds generated for 'chain 'D' and resid 387 through 390' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 435 through 441 Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 495 through 505 removed outlier: 3.942A pdb=" N GLN D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 513 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 541 through 559 removed outlier: 4.254A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 589 No H-bonds generated for 'chain 'D' and resid 587 through 589' Processing helix chain 'D' and resid 631 through 645 Processing helix chain 'D' and resid 649 through 651 No H-bonds generated for 'chain 'D' and resid 649 through 651' Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 748 through 751 No H-bonds generated for 'chain 'D' and resid 748 through 751' Processing helix chain 'D' and resid 762 through 766 Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.662A pdb=" N ARG E 32 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 142 removed outlier: 3.568A pdb=" N HIS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'E' and resid 187 through 222 Processing helix chain 'E' and resid 225 through 233 Processing helix chain 'E' and resid 240 through 255 removed outlier: 3.505A pdb=" N SER E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 272 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.953A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 4.480A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 371 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 435 through 443 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 559 Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 632 through 645 Processing helix chain 'E' and resid 649 through 651 No H-bonds generated for 'chain 'E' and resid 649 through 651' 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 762 through 766 Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.559A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 138 Processing helix chain 'F' and resid 147 through 152 removed outlier: 3.912A pdb=" N VAL F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 173 through 181 Processing helix chain 'F' and resid 187 through 237 removed outlier: 3.695A pdb=" N LYS F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 255 removed outlier: 4.337A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 271 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 404 through 411 Processing helix chain 'F' and resid 436 through 442 Processing helix chain 'F' and resid 479 through 482 No H-bonds generated for 'chain 'F' and resid 479 through 482' Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 506 through 514 Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'F' and resid 541 through 559 Processing helix chain 'F' and resid 574 through 578 removed outlier: 3.716A pdb=" N LEU F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 574 through 578' Processing helix chain 'F' and resid 631 through 646 Processing helix chain 'F' and resid 648 through 650 No H-bonds generated for 'chain 'F' and resid 648 through 650' Processing helix chain 'F' and resid 680 through 692 Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 737 through 745 removed outlier: 4.327A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (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 765 No H-bonds generated for 'chain 'F' and resid 762 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 7 through 10 removed outlier: 8.591A pdb=" N ILE A 8 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE A 45 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU A 10 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 47 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 removed outlier: 7.673A pdb=" N THR A 469 " --> pdb=" O LEU A 353 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.705A pdb=" N VAL A 418 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE A 379 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 420 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 466 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU A 421 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 468 " --> pdb=" O LEU A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.279A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 597 through 603 removed outlier: 3.702A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 613 through 618 removed outlier: 3.916A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 666 " --> pdb=" O GLU A 613 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.287A pdb=" N LYS A 732 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS A 757 " --> pdb=" O LEU A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.509A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 43 through 46 Processing sheet with id= J, first strand: chain 'B' and resid 487 through 489 removed outlier: 6.881A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 379 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 613 through 618 removed outlier: 3.565A pdb=" N GLU B 613 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 664 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 7 through 9 removed outlier: 8.146A pdb=" N ILE C 8 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE C 45 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 82 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 73 through 77 removed outlier: 3.991A pdb=" N GLN C 73 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 352 through 355 Processing sheet with id= O, first strand: chain 'C' and resid 378 through 380 removed outlier: 8.151A pdb=" N ILE C 379 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 420 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 466 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU C 421 " --> pdb=" O PHE C 466 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 468 " --> pdb=" O LEU C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.680A pdb=" N ARG C 567 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 613 through 615 removed outlier: 3.533A pdb=" N GLU C 613 " --> pdb=" O HIS C 666 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 666 " --> pdb=" O GLU C 613 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 700 through 702 removed outlier: 7.062A pdb=" N LYS C 732 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU C 755 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 735 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS C 757 " --> pdb=" O LEU C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= T, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.567A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 43 through 46 Processing sheet with id= V, first strand: chain 'D' and resid 487 through 489 removed outlier: 6.432A pdb=" N VAL D 352 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 351 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE D 419 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.110A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 613 through 618 removed outlier: 3.629A pdb=" N GLU D 613 " --> pdb=" O HIS D 666 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 662 " --> pdb=" O VAL D 617 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 705 through 707 removed outlier: 4.445A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.458A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 21 through 23 removed outlier: 4.055A pdb=" N THR E 21 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 86 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU E 87 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL E 71 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 65 through 67 Processing sheet with id= AC, first strand: chain 'E' and resid 487 through 490 removed outlier: 6.615A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE E 490 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL E 354 " --> pdb=" O ILE E 490 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU E 353 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR E 469 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLY E 355 " --> pdb=" O THR E 469 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA E 471 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 419 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS E 377 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 520 through 522 removed outlier: 5.787A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 613 through 618 removed outlier: 3.783A pdb=" N VAL E 617 " --> pdb=" O ASP E 662 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 665 " --> pdb=" O SER E 624 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 700 through 702 removed outlier: 5.962A pdb=" N LYS E 732 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.956A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN F 68 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG F 91 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY F 66 " --> pdb=" O ARG F 91 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 352 through 354 removed outlier: 9.048A pdb=" N LEU F 353 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR F 469 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 419 " --> pdb=" O PHE F 466 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP F 422 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 520 through 522 removed outlier: 5.775A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 596 through 600 removed outlier: 3.811A pdb=" N HIS F 664 " --> pdb=" O ALA F 615 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 732 through 736 removed outlier: 6.156A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK 1259 hydrogen bonds defined for protein. 3684 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: 13.04 Time building geometry restraints manager: 15.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 12503 1.36 - 1.51: 9595 1.51 - 1.65: 14776 1.65 - 1.80: 183 1.80 - 1.95: 71 Bond restraints: 37128 Sorted by residual: bond pdb=" C ASP D 51 " pdb=" N PRO D 52 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" C ILE A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C ASP C 51 " pdb=" N PRO C 52 " ideal model delta sigma weight residual 1.332 1.379 -0.047 1.33e-02 5.65e+03 1.26e+01 bond pdb=" CA MET B 516 " pdb=" CB MET B 516 " ideal model delta sigma weight residual 1.528 1.573 -0.045 1.47e-02 4.63e+03 9.44e+00 bond pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 8.95e+00 ... (remaining 37123 not shown) Histogram of bond angle deviations from ideal: 92.99 - 101.97: 124 101.97 - 110.95: 12797 110.95 - 119.93: 21109 119.93 - 128.91: 16039 128.91 - 137.89: 255 Bond angle restraints: 50324 Sorted by residual: angle pdb=" CB MET A 439 " pdb=" CG MET A 439 " pdb=" SD MET A 439 " ideal model delta sigma weight residual 112.70 134.77 -22.07 3.00e+00 1.11e-01 5.41e+01 angle pdb=" N THR B 576 " pdb=" CA THR B 576 " pdb=" C THR B 576 " ideal model delta sigma weight residual 114.62 107.02 7.60 1.14e+00 7.69e-01 4.45e+01 angle pdb=" CA GLU D 204 " pdb=" CB GLU D 204 " pdb=" CG GLU D 204 " ideal model delta sigma weight residual 114.10 127.11 -13.01 2.00e+00 2.50e-01 4.23e+01 angle pdb=" N GLN A 229 " pdb=" CA GLN A 229 " pdb=" CB GLN A 229 " ideal model delta sigma weight residual 110.16 119.49 -9.33 1.48e+00 4.57e-01 3.97e+01 angle pdb=" CA ARG F 227 " pdb=" CB ARG F 227 " pdb=" CG ARG F 227 " ideal model delta sigma weight residual 114.10 126.51 -12.41 2.00e+00 2.50e-01 3.85e+01 ... (remaining 50319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 21997 25.17 - 50.34: 867 50.34 - 75.50: 72 75.50 - 100.67: 16 100.67 - 125.84: 2 Dihedral angle restraints: 22954 sinusoidal: 9574 harmonic: 13380 Sorted by residual: dihedral pdb=" CA ALA D 601 " pdb=" C ALA D 601 " pdb=" N TRP D 602 " pdb=" CA TRP D 602 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ASP E 386 " pdb=" C ASP E 386 " pdb=" N GLU E 387 " pdb=" CA GLU E 387 " ideal model delta harmonic sigma weight residual 180.00 150.19 29.81 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA VAL D 706 " pdb=" C VAL D 706 " pdb=" N SER D 707 " pdb=" CA SER D 707 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 22951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4920 0.096 - 0.192: 735 0.192 - 0.288: 61 0.288 - 0.383: 15 0.383 - 0.479: 5 Chirality restraints: 5736 Sorted by residual: chirality pdb=" CG LEU E 249 " pdb=" CB LEU E 249 " pdb=" CD1 LEU E 249 " pdb=" CD2 LEU E 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB ILE F 415 " pdb=" CA ILE F 415 " pdb=" CG1 ILE F 415 " pdb=" CG2 ILE F 415 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.88e+00 ... (remaining 5733 not shown) Planarity restraints: 6548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 534 " 0.045 2.00e-02 2.50e+03 2.99e-02 1.79e+01 pdb=" CG TYR C 534 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR C 534 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 534 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 534 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 534 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 534 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 203 " 0.034 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE F 203 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE F 203 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE F 203 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 203 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 203 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 203 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 602 " -0.026 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP B 602 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 602 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 602 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 602 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 602 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 602 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 602 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 602 " -0.009 2.00e-02 2.50e+03 ... (remaining 6545 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 88 2.37 - 3.00: 17965 3.00 - 3.63: 60234 3.63 - 4.27: 89066 4.27 - 4.90: 139388 Nonbonded interactions: 306741 Sorted by model distance: nonbonded pdb=" O TYR B 320 " pdb=" OH TYR B 493 " model vdw 1.737 2.440 nonbonded pdb=" CD2 TYR B 320 " pdb=" CE2 TYR B 493 " model vdw 2.012 3.640 nonbonded pdb=" OG1 THR E 626 " pdb=" O VAL E 665 " model vdw 2.209 2.440 nonbonded pdb=" OG1 THR D 603 " pdb=" O GLY D 606 " model vdw 2.239 2.440 nonbonded pdb=" O LEU A 290 " pdb=" OG1 THR A 294 " model vdw 2.248 2.440 ... (remaining 306736 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 774) selection = (chain 'B' and resid 2 through 774) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.150 Check model and map are aligned: 0.520 Set scattering table: 0.340 Process input model: 91.860 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.220 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 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 : 0.007 0.098 37128 Z= 0.487 Angle : 1.260 22.072 50324 Z= 0.691 Chirality : 0.068 0.479 5736 Planarity : 0.008 0.074 6548 Dihedral : 13.340 125.839 14338 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 0.13 % Allowed : 0.95 % Favored : 98.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.11), residues: 4626 helix: -1.84 (0.10), residues: 1977 sheet: -2.15 (0.22), residues: 470 loop : -1.89 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP B 602 HIS 0.020 0.003 HIS C 407 PHE 0.065 0.004 PHE F 203 TYR 0.070 0.004 TYR C 534 ARG 0.036 0.002 ARG D 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 296 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.0127 (mtm) cc_final: -0.0293 (mmt) REVERT: A 258 MET cc_start: 0.6309 (mpp) cc_final: 0.5839 (mpp) REVERT: A 306 LEU cc_start: 0.7068 (mt) cc_final: 0.6623 (mt) REVERT: A 650 ASP cc_start: 0.8136 (m-30) cc_final: 0.7870 (t70) REVERT: A 698 MET cc_start: 0.4316 (tpt) cc_final: 0.3292 (mmm) REVERT: B 38 MET cc_start: 0.3624 (mpp) cc_final: 0.2982 (mpp) REVERT: B 160 MET cc_start: 0.8380 (tmm) cc_final: 0.7291 (ppp) REVERT: B 276 MET cc_start: 0.6760 (tpt) cc_final: 0.6464 (tpt) REVERT: B 319 HIS cc_start: 0.7660 (m-70) cc_final: 0.7454 (m-70) REVERT: B 409 MET cc_start: 0.4275 (ppp) cc_final: 0.4011 (ppp) REVERT: B 432 ARG cc_start: 0.6059 (mtm180) cc_final: 0.5464 (tpt-90) REVERT: B 439 MET cc_start: 0.9005 (mpp) cc_final: 0.8778 (mpp) REVERT: C 427 MET cc_start: 0.6678 (tmm) cc_final: 0.6252 (tpp) REVERT: D 75 MET cc_start: 0.3834 (pmm) cc_final: 0.2185 (ptt) REVERT: D 160 MET cc_start: 0.7609 (ppp) cc_final: 0.7328 (ppp) REVERT: D 258 MET cc_start: 0.4488 (mtt) cc_final: 0.3959 (mtt) REVERT: D 419 ILE cc_start: 0.3551 (mm) cc_final: 0.3213 (mt) REVERT: D 439 MET cc_start: 0.8762 (ppp) cc_final: 0.8534 (ppp) REVERT: D 634 LYS cc_start: 0.8177 (mttp) cc_final: 0.7977 (mmtt) REVERT: D 691 LEU cc_start: 0.6326 (mp) cc_final: 0.6064 (tp) REVERT: E 85 MET cc_start: 0.1712 (tpt) cc_final: 0.1268 (ptp) REVERT: E 421 LEU cc_start: 0.7659 (mm) cc_final: 0.7369 (mt) REVERT: E 713 MET cc_start: 0.7581 (ppp) cc_final: 0.7235 (ppp) REVERT: F 401 MET cc_start: 0.8127 (tpt) cc_final: 0.7629 (tmm) REVERT: F 427 MET cc_start: 0.5869 (tpt) cc_final: 0.4800 (tpt) REVERT: F 583 TYR cc_start: 0.7395 (m-80) cc_final: 0.7163 (m-10) REVERT: F 633 MET cc_start: 0.8580 (ttt) cc_final: 0.8127 (ptp) REVERT: F 698 MET cc_start: 0.0775 (mmt) cc_final: -0.1162 (mmt) outliers start: 5 outliers final: 2 residues processed: 300 average time/residue: 0.5058 time to fit residues: 246.5478 Evaluate side-chains 243 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain D residue 350 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 0.5980 chunk 350 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 419 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 727 GLN C 83 GLN C 659 ASN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37128 Z= 0.178 Angle : 0.663 13.253 50324 Z= 0.336 Chirality : 0.044 0.185 5736 Planarity : 0.005 0.063 6548 Dihedral : 7.152 127.908 5144 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.56 % Allowed : 7.14 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.12), residues: 4626 helix: -0.79 (0.11), residues: 1959 sheet: -1.95 (0.22), residues: 492 loop : -1.70 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 431 HIS 0.007 0.001 HIS C 454 PHE 0.030 0.001 PHE F 203 TYR 0.028 0.001 TYR B 320 ARG 0.008 0.000 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 261 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: -0.0218 (mtm) cc_final: -0.0720 (mmt) REVERT: A 258 MET cc_start: 0.6742 (mpp) cc_final: 0.5938 (mpp) REVERT: A 306 LEU cc_start: 0.6986 (mt) cc_final: 0.6543 (mt) REVERT: A 381 LEU cc_start: 0.9551 (mt) cc_final: 0.8833 (tt) REVERT: A 409 MET cc_start: 0.9620 (mmp) cc_final: 0.8643 (tmm) REVERT: A 427 MET cc_start: 0.6979 (ptt) cc_final: 0.6679 (tmm) REVERT: A 650 ASP cc_start: 0.8127 (m-30) cc_final: 0.7810 (t70) REVERT: A 698 MET cc_start: 0.4339 (tpt) cc_final: 0.2996 (mmm) REVERT: B 38 MET cc_start: 0.3533 (mpp) cc_final: 0.3129 (mpp) REVERT: B 218 ASP cc_start: 0.9098 (t70) cc_final: 0.8852 (m-30) REVERT: B 276 MET cc_start: 0.6795 (tpt) cc_final: 0.6496 (tpt) REVERT: B 409 MET cc_start: 0.4036 (ppp) cc_final: 0.3740 (ppp) REVERT: B 496 MET cc_start: 0.8414 (tmm) cc_final: 0.8177 (tmm) REVERT: C 230 MET cc_start: -0.2026 (ptt) cc_final: -0.2259 (ptt) REVERT: C 401 MET cc_start: 0.6362 (mmm) cc_final: 0.5708 (mmm) REVERT: C 762 VAL cc_start: 0.5861 (t) cc_final: 0.5459 (t) REVERT: D 75 MET cc_start: 0.4188 (pmm) cc_final: 0.2187 (ptt) REVERT: D 160 MET cc_start: 0.7596 (ppp) cc_final: 0.7322 (ppp) REVERT: D 361 LYS cc_start: 0.7602 (mttt) cc_final: 0.6434 (ptpt) REVERT: D 439 MET cc_start: 0.9261 (ppp) cc_final: 0.8997 (ppp) REVERT: D 552 ARG cc_start: 0.7040 (mmm160) cc_final: 0.5202 (mmp80) REVERT: D 663 LEU cc_start: 0.7374 (tt) cc_final: 0.7056 (tp) REVERT: D 691 LEU cc_start: 0.6223 (mp) cc_final: 0.5895 (tp) REVERT: D 713 MET cc_start: 0.7795 (tmm) cc_final: 0.7472 (tmm) REVERT: E 75 MET cc_start: -0.1835 (mpp) cc_final: -0.2050 (mpp) REVERT: E 401 MET cc_start: 0.8405 (tpp) cc_final: 0.7609 (ppp) REVERT: E 683 MET cc_start: 0.3535 (mpp) cc_final: 0.3207 (mpp) REVERT: E 713 MET cc_start: 0.7321 (ppp) cc_final: 0.7078 (ppp) REVERT: F 276 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7575 (ppp) REVERT: F 427 MET cc_start: 0.5666 (tpt) cc_final: 0.4896 (tpt) REVERT: F 583 TYR cc_start: 0.7420 (m-80) cc_final: 0.7190 (m-10) REVERT: F 698 MET cc_start: 0.1365 (mmt) cc_final: 0.1162 (mmt) outliers start: 22 outliers final: 14 residues processed: 271 average time/residue: 0.5024 time to fit residues: 224.1960 Evaluate side-chains 246 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 231 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 307 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 420 optimal weight: 7.9990 chunk 454 optimal weight: 9.9990 chunk 374 optimal weight: 0.7980 chunk 416 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 337 optimal weight: 3.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN C 664 HIS D 499 GLN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS E 495 ASN ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 37128 Z= 0.293 Angle : 0.733 12.396 50324 Z= 0.372 Chirality : 0.046 0.175 5736 Planarity : 0.006 0.057 6548 Dihedral : 7.036 120.613 5142 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.54 % Allowed : 10.09 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.95 (0.12), residues: 4626 helix: -0.64 (0.11), residues: 1975 sheet: -2.06 (0.22), residues: 505 loop : -1.64 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 431 HIS 0.012 0.002 HIS E 666 PHE 0.025 0.002 PHE F 203 TYR 0.021 0.002 TYR E 332 ARG 0.008 0.001 ARG C 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 249 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6980 (mpp) cc_final: 0.6062 (mpp) REVERT: A 381 LEU cc_start: 0.9583 (mt) cc_final: 0.8964 (tp) REVERT: A 427 MET cc_start: 0.6989 (ptt) cc_final: 0.6424 (tmm) REVERT: A 650 ASP cc_start: 0.8261 (m-30) cc_final: 0.7980 (t70) REVERT: B 38 MET cc_start: 0.3813 (mpp) cc_final: 0.3403 (mpp) REVERT: B 160 MET cc_start: 0.8024 (tmm) cc_final: 0.6526 (ppp) REVERT: B 496 MET cc_start: 0.8496 (tmm) cc_final: 0.8206 (tmm) REVERT: B 545 ARG cc_start: 0.7701 (mmt180) cc_final: 0.6837 (ptt90) REVERT: C 230 MET cc_start: -0.1656 (ptt) cc_final: -0.1869 (ptt) REVERT: C 401 MET cc_start: 0.6708 (mmm) cc_final: 0.6035 (mmm) REVERT: D 75 MET cc_start: 0.4380 (pmm) cc_final: 0.3979 (pmm) REVERT: D 160 MET cc_start: 0.7678 (ppp) cc_final: 0.7440 (ppp) REVERT: D 427 MET cc_start: 0.8323 (mmm) cc_final: 0.7240 (tmm) REVERT: D 439 MET cc_start: 0.9380 (ppp) cc_final: 0.9057 (ppp) REVERT: D 552 ARG cc_start: 0.7417 (mmm160) cc_final: 0.5888 (mmp80) REVERT: D 713 MET cc_start: 0.8094 (tmm) cc_final: 0.7400 (tmm) REVERT: E 75 MET cc_start: -0.1916 (mpp) cc_final: -0.2422 (mpp) REVERT: E 390 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8794 (tt) REVERT: E 401 MET cc_start: 0.8597 (tpp) cc_final: 0.7799 (ppp) REVERT: E 439 MET cc_start: 0.8650 (mmm) cc_final: 0.8254 (mmt) REVERT: E 713 MET cc_start: 0.7550 (ppp) cc_final: 0.7060 (ppp) REVERT: F 328 ARG cc_start: 0.7860 (mpt180) cc_final: 0.7454 (tpt170) REVERT: F 427 MET cc_start: 0.6306 (tpt) cc_final: 0.5757 (tpt) REVERT: F 583 TYR cc_start: 0.7418 (m-80) cc_final: 0.7192 (m-10) REVERT: F 698 MET cc_start: 0.1353 (mmt) cc_final: 0.1096 (mmt) outliers start: 60 outliers final: 34 residues processed: 284 average time/residue: 0.4813 time to fit residues: 227.0483 Evaluate side-chains 268 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 233 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 664 HIS Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 307 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 50.0000 chunk 316 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 282 optimal weight: 10.0000 chunk 421 optimal weight: 5.9990 chunk 446 optimal weight: 40.0000 chunk 220 optimal weight: 4.9990 chunk 399 optimal weight: 40.0000 chunk 120 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 407 HIS A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 37128 Z= 0.274 Angle : 0.704 11.149 50324 Z= 0.359 Chirality : 0.045 0.183 5736 Planarity : 0.005 0.056 6548 Dihedral : 6.928 119.593 5142 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.68 % Favored : 93.30 % Rotamer: Outliers : 2.11 % Allowed : 12.28 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.87 (0.12), residues: 4626 helix: -0.51 (0.11), residues: 1977 sheet: -2.18 (0.22), residues: 515 loop : -1.63 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 431 HIS 0.020 0.002 HIS C 664 PHE 0.021 0.002 PHE F 203 TYR 0.022 0.002 TYR C 332 ARG 0.008 0.001 ARG D 552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 240 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.7045 (mpp) cc_final: 0.6242 (mpp) REVERT: A 381 LEU cc_start: 0.9523 (mt) cc_final: 0.8876 (tp) REVERT: A 409 MET cc_start: 0.9571 (mmm) cc_final: 0.8604 (tmm) REVERT: A 427 MET cc_start: 0.6954 (ptt) cc_final: 0.6359 (tmm) REVERT: A 650 ASP cc_start: 0.8258 (m-30) cc_final: 0.7954 (t70) REVERT: B 38 MET cc_start: 0.3942 (mpp) cc_final: 0.3442 (mpp) REVERT: B 160 MET cc_start: 0.7988 (tmm) cc_final: 0.6431 (ppp) REVERT: B 409 MET cc_start: 0.4056 (ppp) cc_final: 0.3802 (ppp) REVERT: B 496 MET cc_start: 0.8585 (tmm) cc_final: 0.8304 (tmm) REVERT: B 545 ARG cc_start: 0.7732 (mmt180) cc_final: 0.6940 (ptt90) REVERT: C 217 MET cc_start: 0.6989 (tpt) cc_final: 0.5826 (mmm) REVERT: C 401 MET cc_start: 0.6503 (mmm) cc_final: 0.5927 (mmm) REVERT: C 664 HIS cc_start: 0.7867 (m170) cc_final: 0.7579 (m-70) REVERT: D 75 MET cc_start: 0.4361 (pmm) cc_final: 0.3954 (pmm) REVERT: D 160 MET cc_start: 0.7712 (ppp) cc_final: 0.7477 (ppp) REVERT: D 258 MET cc_start: 0.3656 (mtt) cc_final: 0.2813 (mtt) REVERT: D 276 MET cc_start: 0.1211 (mpp) cc_final: -0.0025 (mpp) REVERT: D 439 MET cc_start: 0.9372 (ppp) cc_final: 0.9115 (ppp) REVERT: D 552 ARG cc_start: 0.7323 (mmm160) cc_final: 0.5888 (mmp80) REVERT: E 75 MET cc_start: -0.2137 (mpp) cc_final: -0.2667 (mpp) REVERT: E 439 MET cc_start: 0.8691 (mmm) cc_final: 0.8308 (mmt) REVERT: E 633 MET cc_start: 0.8354 (mmm) cc_final: 0.8009 (mmm) REVERT: E 683 MET cc_start: 0.4799 (OUTLIER) cc_final: 0.4401 (mtp) REVERT: E 713 MET cc_start: 0.7506 (ppp) cc_final: 0.6949 (ppp) REVERT: F 328 ARG cc_start: 0.7908 (mpt180) cc_final: 0.7415 (tpt170) REVERT: F 427 MET cc_start: 0.6374 (tpt) cc_final: 0.5951 (tpt) REVERT: F 496 MET cc_start: 0.6034 (pmm) cc_final: 0.4988 (pmm) REVERT: F 583 TYR cc_start: 0.7485 (m-80) cc_final: 0.7222 (m-10) REVERT: F 698 MET cc_start: 0.1782 (mmt) cc_final: 0.1523 (mmt) outliers start: 82 outliers final: 51 residues processed: 299 average time/residue: 0.4714 time to fit residues: 235.5161 Evaluate side-chains 277 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 225 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 319 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 0.9990 chunk 253 optimal weight: 0.7980 chunk 6 optimal weight: 50.0000 chunk 332 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 381 optimal weight: 9.9990 chunk 308 optimal weight: 60.0000 chunk 0 optimal weight: 50.0000 chunk 228 optimal weight: 10.0000 chunk 400 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 221 GLN ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37128 Z= 0.207 Angle : 0.650 12.102 50324 Z= 0.326 Chirality : 0.044 0.181 5736 Planarity : 0.005 0.066 6548 Dihedral : 6.694 117.140 5142 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.75 % Allowed : 14.28 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.65 (0.12), residues: 4626 helix: -0.26 (0.11), residues: 1968 sheet: -2.12 (0.22), residues: 510 loop : -1.56 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 431 HIS 0.008 0.001 HIS E 666 PHE 0.017 0.001 PHE F 203 TYR 0.033 0.002 TYR D 225 ARG 0.005 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 232 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6998 (mpp) cc_final: 0.6311 (mpp) REVERT: A 378 ARG cc_start: 0.9173 (ttt90) cc_final: 0.8973 (ttt90) REVERT: A 381 LEU cc_start: 0.9493 (mt) cc_final: 0.8836 (tp) REVERT: A 409 MET cc_start: 0.9621 (mmm) cc_final: 0.8721 (tmm) REVERT: A 427 MET cc_start: 0.6893 (ptt) cc_final: 0.6338 (tmm) REVERT: A 650 ASP cc_start: 0.8200 (m-30) cc_final: 0.7815 (t0) REVERT: A 698 MET cc_start: 0.4161 (tpt) cc_final: 0.2796 (mmm) REVERT: A 702 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.5132 (tmm) REVERT: B 38 MET cc_start: 0.3979 (mpp) cc_final: 0.3468 (mpp) REVERT: B 319 HIS cc_start: 0.7675 (m-70) cc_final: 0.7463 (m170) REVERT: B 496 MET cc_start: 0.8595 (tmm) cc_final: 0.8272 (tmm) REVERT: B 698 MET cc_start: 0.8131 (ptm) cc_final: 0.7674 (pmm) REVERT: C 401 MET cc_start: 0.6417 (mmm) cc_final: 0.5943 (mmm) REVERT: D 75 MET cc_start: 0.4387 (pmm) cc_final: 0.3985 (pmm) REVERT: D 160 MET cc_start: 0.7772 (ppp) cc_final: 0.7532 (ppp) REVERT: D 258 MET cc_start: 0.3799 (mtt) cc_final: 0.3058 (mtt) REVERT: D 427 MET cc_start: 0.8322 (mmm) cc_final: 0.7408 (tmm) REVERT: D 439 MET cc_start: 0.9399 (ppp) cc_final: 0.9018 (ppp) REVERT: D 552 ARG cc_start: 0.7312 (mmm160) cc_final: 0.5738 (mmp80) REVERT: D 713 MET cc_start: 0.8174 (tmm) cc_final: 0.7482 (tmm) REVERT: E 85 MET cc_start: 0.2360 (ptt) cc_final: 0.2138 (tpt) REVERT: E 401 MET cc_start: 0.8256 (tpp) cc_final: 0.7459 (ppp) REVERT: E 439 MET cc_start: 0.8834 (mmm) cc_final: 0.8591 (mmt) REVERT: E 683 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4445 (mtp) REVERT: E 713 MET cc_start: 0.7074 (ppp) cc_final: 0.6623 (ppp) REVERT: F 222 ARG cc_start: 0.9261 (mmp-170) cc_final: 0.9019 (mmp80) REVERT: F 328 ARG cc_start: 0.7918 (mpt180) cc_final: 0.7407 (tpt170) REVERT: F 416 ASN cc_start: 0.6356 (OUTLIER) cc_final: 0.5804 (p0) REVERT: F 427 MET cc_start: 0.6229 (tpt) cc_final: 0.5720 (tpt) REVERT: F 496 MET cc_start: 0.6065 (pmm) cc_final: 0.5064 (pmm) REVERT: F 583 TYR cc_start: 0.7498 (m-80) cc_final: 0.7256 (m-10) REVERT: F 698 MET cc_start: 0.1705 (mmt) cc_final: 0.1468 (mmt) outliers start: 68 outliers final: 47 residues processed: 281 average time/residue: 0.4951 time to fit residues: 231.1754 Evaluate side-chains 277 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 227 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain F residue 416 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 4.9990 chunk 402 optimal weight: 10.0000 chunk 88 optimal weight: 0.1980 chunk 262 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 447 optimal weight: 8.9990 chunk 371 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 234 optimal weight: 30.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 340 GLN A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37128 Z= 0.213 Angle : 0.651 12.303 50324 Z= 0.325 Chirality : 0.044 0.181 5736 Planarity : 0.005 0.058 6548 Dihedral : 6.567 113.896 5142 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.79 % Favored : 93.19 % Rotamer: Outliers : 2.26 % Allowed : 14.89 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.53 (0.12), residues: 4626 helix: -0.14 (0.11), residues: 1969 sheet: -2.05 (0.22), residues: 500 loop : -1.53 (0.14), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 431 HIS 0.008 0.001 HIS A 666 PHE 0.016 0.001 PHE F 203 TYR 0.035 0.001 TYR D 225 ARG 0.017 0.000 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 240 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6968 (mpp) cc_final: 0.6339 (mpp) REVERT: A 381 LEU cc_start: 0.9494 (mt) cc_final: 0.8814 (tp) REVERT: A 409 MET cc_start: 0.9596 (mmm) cc_final: 0.8717 (tmm) REVERT: A 427 MET cc_start: 0.6871 (ptt) cc_final: 0.6340 (tmm) REVERT: A 516 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.6017 (ppp) REVERT: A 534 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5149 (m-10) REVERT: A 650 ASP cc_start: 0.8223 (m-30) cc_final: 0.7835 (t0) REVERT: A 702 MET cc_start: 0.5245 (OUTLIER) cc_final: 0.4842 (tmm) REVERT: B 409 MET cc_start: 0.4206 (ppp) cc_final: 0.3962 (ppp) REVERT: B 496 MET cc_start: 0.8616 (tmm) cc_final: 0.8281 (tmm) REVERT: C 217 MET cc_start: 0.7034 (tpt) cc_final: 0.5901 (mmm) REVERT: C 401 MET cc_start: 0.6362 (mmm) cc_final: 0.5949 (mmm) REVERT: D 160 MET cc_start: 0.7806 (ppp) cc_final: 0.7569 (ppp) REVERT: D 204 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: D 258 MET cc_start: 0.3825 (mtt) cc_final: 0.3061 (mtt) REVERT: D 427 MET cc_start: 0.8354 (mmm) cc_final: 0.7375 (tmm) REVERT: D 439 MET cc_start: 0.9422 (ppp) cc_final: 0.9051 (ppp) REVERT: D 552 ARG cc_start: 0.7306 (mmm160) cc_final: 0.5779 (mmp80) REVERT: D 691 LEU cc_start: 0.6529 (mp) cc_final: 0.6144 (mt) REVERT: D 713 MET cc_start: 0.8133 (tmm) cc_final: 0.7333 (tmm) REVERT: E 276 MET cc_start: 0.8046 (mpp) cc_final: 0.7581 (mpp) REVERT: E 401 MET cc_start: 0.8295 (tpp) cc_final: 0.7505 (ppp) REVERT: E 439 MET cc_start: 0.8832 (mmm) cc_final: 0.8578 (mmm) REVERT: E 683 MET cc_start: 0.4854 (OUTLIER) cc_final: 0.4488 (mtp) REVERT: E 713 MET cc_start: 0.7018 (ppp) cc_final: 0.6588 (ppp) REVERT: F 328 ARG cc_start: 0.7938 (mpt180) cc_final: 0.7389 (tpt170) REVERT: F 416 ASN cc_start: 0.6334 (OUTLIER) cc_final: 0.5796 (p0) REVERT: F 427 MET cc_start: 0.6331 (tpt) cc_final: 0.5852 (tpt) REVERT: F 496 MET cc_start: 0.6113 (pmm) cc_final: 0.5131 (pmm) REVERT: F 583 TYR cc_start: 0.7566 (m-80) cc_final: 0.7322 (m-10) outliers start: 88 outliers final: 64 residues processed: 301 average time/residue: 0.4695 time to fit residues: 235.3592 Evaluate side-chains 303 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 233 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 416 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 254 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 376 optimal weight: 9.9990 chunk 249 optimal weight: 50.0000 chunk 445 optimal weight: 20.0000 chunk 278 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 319 HIS ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 HIS ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37128 Z= 0.224 Angle : 0.662 12.183 50324 Z= 0.331 Chirality : 0.044 0.187 5736 Planarity : 0.005 0.065 6548 Dihedral : 6.515 111.637 5142 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.75 % Allowed : 15.20 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.50 (0.12), residues: 4626 helix: -0.10 (0.11), residues: 1967 sheet: -2.02 (0.22), residues: 508 loop : -1.53 (0.14), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 602 HIS 0.008 0.001 HIS A 666 PHE 0.015 0.001 PHE F 203 TYR 0.033 0.002 TYR D 225 ARG 0.010 0.000 ARG E 484 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 238 time to evaluate : 4.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6986 (mpp) cc_final: 0.6401 (mpp) REVERT: A 381 LEU cc_start: 0.9487 (mt) cc_final: 0.8786 (tp) REVERT: A 409 MET cc_start: 0.9599 (mmm) cc_final: 0.8634 (tmm) REVERT: A 427 MET cc_start: 0.6759 (ptt) cc_final: 0.6240 (tmm) REVERT: A 516 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.6051 (ppp) REVERT: A 534 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.5153 (m-10) REVERT: A 650 ASP cc_start: 0.8292 (m-30) cc_final: 0.7918 (t0) REVERT: A 698 MET cc_start: 0.4137 (tpt) cc_final: 0.2718 (mmm) REVERT: B 38 MET cc_start: 0.3236 (mmt) cc_final: 0.2413 (mpp) REVERT: B 409 MET cc_start: 0.4337 (ppp) cc_final: 0.4022 (ppp) REVERT: B 496 MET cc_start: 0.8625 (tmm) cc_final: 0.8312 (tmm) REVERT: B 545 ARG cc_start: 0.7744 (mmt180) cc_final: 0.7030 (ptt90) REVERT: B 698 MET cc_start: 0.8131 (ptm) cc_final: 0.7844 (pmm) REVERT: C 217 MET cc_start: 0.7009 (tpt) cc_final: 0.5848 (mmm) REVERT: C 401 MET cc_start: 0.6036 (mmm) cc_final: 0.5625 (mmm) REVERT: D 160 MET cc_start: 0.7793 (ppp) cc_final: 0.7562 (ppp) REVERT: D 258 MET cc_start: 0.3975 (mtt) cc_final: 0.3380 (mtm) REVERT: D 427 MET cc_start: 0.8287 (mmm) cc_final: 0.7250 (tmm) REVERT: D 439 MET cc_start: 0.9427 (ppp) cc_final: 0.9084 (ppp) REVERT: D 552 ARG cc_start: 0.7240 (mmm160) cc_final: 0.5321 (mmp80) REVERT: D 691 LEU cc_start: 0.6598 (mp) cc_final: 0.6230 (mt) REVERT: D 713 MET cc_start: 0.8183 (tmm) cc_final: 0.7326 (tmm) REVERT: E 85 MET cc_start: 0.1514 (tpt) cc_final: 0.0823 (ptt) REVERT: E 401 MET cc_start: 0.8338 (tpp) cc_final: 0.7587 (ppp) REVERT: E 439 MET cc_start: 0.8901 (mmm) cc_final: 0.8672 (mmm) REVERT: E 683 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.4688 (mtm) REVERT: E 713 MET cc_start: 0.6991 (ppp) cc_final: 0.6543 (ppp) REVERT: F 328 ARG cc_start: 0.7998 (mpt180) cc_final: 0.7465 (tpt90) REVERT: F 427 MET cc_start: 0.6344 (tpt) cc_final: 0.5934 (tpt) REVERT: F 496 MET cc_start: 0.6196 (pmm) cc_final: 0.5222 (pmm) REVERT: F 583 TYR cc_start: 0.7524 (m-80) cc_final: 0.7270 (m-10) REVERT: F 658 TYR cc_start: 0.8088 (t80) cc_final: 0.6974 (p90) outliers start: 107 outliers final: 81 residues processed: 318 average time/residue: 0.4843 time to fit residues: 255.2494 Evaluate side-chains 316 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 232 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 265 optimal weight: 0.0270 chunk 134 optimal weight: 2.9990 chunk 87 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 ASN ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 37128 Z= 0.238 Angle : 0.679 12.355 50324 Z= 0.340 Chirality : 0.044 0.191 5736 Planarity : 0.005 0.063 6548 Dihedral : 6.505 110.168 5142 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.67 % Allowed : 15.64 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.47 (0.12), residues: 4626 helix: -0.08 (0.12), residues: 1951 sheet: -1.97 (0.23), residues: 494 loop : -1.53 (0.14), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 602 HIS 0.008 0.001 HIS A 666 PHE 0.016 0.001 PHE F 451 TYR 0.027 0.002 TYR C 332 ARG 0.007 0.000 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 241 time to evaluate : 5.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6948 (mpp) cc_final: 0.6435 (mpp) REVERT: A 381 LEU cc_start: 0.9500 (mt) cc_final: 0.8769 (tp) REVERT: A 401 MET cc_start: 0.9479 (tpp) cc_final: 0.8788 (mmp) REVERT: A 409 MET cc_start: 0.9582 (mmm) cc_final: 0.8711 (tmm) REVERT: A 427 MET cc_start: 0.6733 (ptt) cc_final: 0.6244 (tmm) REVERT: A 516 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.6107 (ppp) REVERT: A 534 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.5063 (m-10) REVERT: A 650 ASP cc_start: 0.8298 (m-30) cc_final: 0.7948 (t0) REVERT: B 38 MET cc_start: 0.3087 (mmt) cc_final: 0.2238 (mpp) REVERT: B 409 MET cc_start: 0.4282 (ppp) cc_final: 0.3995 (ppp) REVERT: B 496 MET cc_start: 0.8662 (tmm) cc_final: 0.8355 (tmm) REVERT: B 545 ARG cc_start: 0.7733 (mmt180) cc_final: 0.7039 (ptt90) REVERT: B 698 MET cc_start: 0.8132 (ptm) cc_final: 0.7883 (pmm) REVERT: C 217 MET cc_start: 0.7021 (tpt) cc_final: 0.5835 (mmm) REVERT: D 160 MET cc_start: 0.7802 (ppp) cc_final: 0.7571 (ppp) REVERT: D 220 ASN cc_start: 0.7737 (m-40) cc_final: 0.7527 (m110) REVERT: D 258 MET cc_start: 0.3991 (mtt) cc_final: 0.2556 (ttm) REVERT: D 427 MET cc_start: 0.8259 (mmm) cc_final: 0.7200 (tmm) REVERT: D 439 MET cc_start: 0.9436 (ppp) cc_final: 0.9105 (ppp) REVERT: D 552 ARG cc_start: 0.7394 (mmm160) cc_final: 0.5448 (mmp80) REVERT: E 85 MET cc_start: 0.1367 (tpt) cc_final: 0.0661 (ptt) REVERT: E 276 MET cc_start: 0.7952 (mpp) cc_final: 0.7604 (mpp) REVERT: E 351 LEU cc_start: 0.8731 (tp) cc_final: 0.8505 (mt) REVERT: E 439 MET cc_start: 0.8880 (mmm) cc_final: 0.8648 (mmm) REVERT: E 683 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4820 (mtm) REVERT: E 713 MET cc_start: 0.6933 (ppp) cc_final: 0.6247 (ppp) REVERT: F 233 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7456 (tt) REVERT: F 328 ARG cc_start: 0.8033 (mpt180) cc_final: 0.7484 (tpt90) REVERT: F 416 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.5957 (p0) REVERT: F 427 MET cc_start: 0.6356 (tpt) cc_final: 0.5961 (tpt) REVERT: F 496 MET cc_start: 0.6120 (pmm) cc_final: 0.5102 (pmm) REVERT: F 583 TYR cc_start: 0.7578 (m-80) cc_final: 0.7328 (m-10) REVERT: F 658 TYR cc_start: 0.8080 (t80) cc_final: 0.6897 (p90) REVERT: F 698 MET cc_start: 0.1835 (mmt) cc_final: 0.0141 (mmt) outliers start: 104 outliers final: 83 residues processed: 319 average time/residue: 0.4748 time to fit residues: 252.8445 Evaluate side-chains 322 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 234 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 10.0000 chunk 426 optimal weight: 1.9990 chunk 389 optimal weight: 50.0000 chunk 414 optimal weight: 0.9990 chunk 249 optimal weight: 40.0000 chunk 180 optimal weight: 40.0000 chunk 325 optimal weight: 50.0000 chunk 127 optimal weight: 7.9990 chunk 374 optimal weight: 8.9990 chunk 392 optimal weight: 50.0000 chunk 413 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 GLN ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37128 Z= 0.272 Angle : 0.721 12.333 50324 Z= 0.361 Chirality : 0.045 0.256 5736 Planarity : 0.005 0.066 6548 Dihedral : 6.608 109.207 5142 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 31.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.65 % Allowed : 16.18 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.62 (0.12), residues: 4626 helix: -0.19 (0.11), residues: 1950 sheet: -2.08 (0.22), residues: 519 loop : -1.58 (0.14), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 602 HIS 0.009 0.002 HIS D 664 PHE 0.021 0.002 PHE F 451 TYR 0.039 0.002 TYR C 658 ARG 0.007 0.001 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 239 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6936 (mpp) cc_final: 0.6595 (mpp) REVERT: A 381 LEU cc_start: 0.9516 (mt) cc_final: 0.9031 (mt) REVERT: A 401 MET cc_start: 0.9449 (tpp) cc_final: 0.8763 (mmm) REVERT: A 409 MET cc_start: 0.9581 (mmm) cc_final: 0.9176 (mmm) REVERT: A 427 MET cc_start: 0.6696 (ptt) cc_final: 0.5848 (mmm) REVERT: A 516 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.6180 (ppp) REVERT: A 534 TYR cc_start: 0.6421 (OUTLIER) cc_final: 0.5036 (m-10) REVERT: A 650 ASP cc_start: 0.8372 (m-30) cc_final: 0.8043 (t0) REVERT: A 698 MET cc_start: 0.4627 (tpt) cc_final: 0.3508 (mmm) REVERT: B 38 MET cc_start: 0.3007 (mmt) cc_final: 0.2174 (mpp) REVERT: B 409 MET cc_start: 0.4368 (ppp) cc_final: 0.4033 (ppp) REVERT: B 496 MET cc_start: 0.8700 (tmm) cc_final: 0.8390 (tmm) REVERT: B 545 ARG cc_start: 0.7693 (mmt180) cc_final: 0.7032 (ptt90) REVERT: B 635 GLU cc_start: 0.8258 (tp30) cc_final: 0.7895 (tp30) REVERT: C 254 GLU cc_start: 0.2626 (OUTLIER) cc_final: 0.2055 (mt-10) REVERT: D 160 MET cc_start: 0.7851 (ppp) cc_final: 0.7623 (ppp) REVERT: D 220 ASN cc_start: 0.7796 (m-40) cc_final: 0.7592 (m110) REVERT: D 258 MET cc_start: 0.3915 (mtt) cc_final: 0.2539 (ttm) REVERT: D 372 MET cc_start: 0.7885 (ptp) cc_final: 0.7521 (ptp) REVERT: D 427 MET cc_start: 0.8280 (mmm) cc_final: 0.7296 (tmm) REVERT: D 439 MET cc_start: 0.9456 (ppp) cc_final: 0.9162 (ppp) REVERT: D 552 ARG cc_start: 0.7496 (mmm160) cc_final: 0.5528 (mmp80) REVERT: E 85 MET cc_start: 0.1216 (tpt) cc_final: 0.0705 (ptt) REVERT: E 276 MET cc_start: 0.7974 (mpp) cc_final: 0.7662 (mpp) REVERT: E 351 LEU cc_start: 0.8745 (tp) cc_final: 0.8469 (mt) REVERT: E 401 MET cc_start: 0.8614 (mmm) cc_final: 0.7910 (ppp) REVERT: E 439 MET cc_start: 0.8859 (mmm) cc_final: 0.8630 (mmm) REVERT: E 683 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.5093 (mtp) REVERT: E 713 MET cc_start: 0.6445 (ppp) cc_final: 0.6116 (ppp) REVERT: F 328 ARG cc_start: 0.7929 (mpt180) cc_final: 0.7392 (tpt90) REVERT: F 427 MET cc_start: 0.6522 (tpt) cc_final: 0.6229 (tpt) REVERT: F 475 GLN cc_start: 0.7991 (mp10) cc_final: 0.7581 (mp10) REVERT: F 496 MET cc_start: 0.6286 (pmm) cc_final: 0.5283 (pmm) REVERT: F 583 TYR cc_start: 0.7589 (m-80) cc_final: 0.7321 (m-10) outliers start: 103 outliers final: 88 residues processed: 314 average time/residue: 0.4793 time to fit residues: 249.6076 Evaluate side-chains 325 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 233 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 332 TYR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 5.9990 chunk 438 optimal weight: 30.0000 chunk 267 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 305 optimal weight: 0.2980 chunk 460 optimal weight: 7.9990 chunk 423 optimal weight: 8.9990 chunk 366 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 283 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 37128 Z= 0.332 Angle : 0.812 59.200 50324 Z= 0.426 Chirality : 0.049 0.781 5736 Planarity : 0.005 0.067 6548 Dihedral : 6.607 109.239 5142 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 33.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.62 % Allowed : 16.54 % Favored : 80.84 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.63 (0.12), residues: 4626 helix: -0.21 (0.11), residues: 1950 sheet: -2.06 (0.22), residues: 532 loop : -1.58 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 602 HIS 0.008 0.001 HIS E 666 PHE 0.028 0.002 PHE C 451 TYR 0.026 0.002 TYR D 225 ARG 0.022 0.000 ARG B 697 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 235 time to evaluate : 4.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6934 (mpp) cc_final: 0.6595 (mpp) REVERT: A 381 LEU cc_start: 0.9517 (mt) cc_final: 0.9031 (mt) REVERT: A 401 MET cc_start: 0.9445 (tpp) cc_final: 0.8762 (mmm) REVERT: A 409 MET cc_start: 0.9556 (mmm) cc_final: 0.9148 (mmm) REVERT: A 415 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8020 (pt) REVERT: A 427 MET cc_start: 0.6695 (ptt) cc_final: 0.5846 (mmm) REVERT: A 516 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6178 (ppp) REVERT: A 534 TYR cc_start: 0.6414 (OUTLIER) cc_final: 0.5030 (m-10) REVERT: A 650 ASP cc_start: 0.8376 (m-30) cc_final: 0.8040 (t0) REVERT: A 698 MET cc_start: 0.4619 (tpt) cc_final: 0.3505 (mmm) REVERT: B 38 MET cc_start: 0.3014 (mmt) cc_final: 0.2182 (mpp) REVERT: B 409 MET cc_start: 0.4363 (ppp) cc_final: 0.4016 (ppp) REVERT: B 496 MET cc_start: 0.8698 (tmm) cc_final: 0.8389 (tmm) REVERT: B 545 ARG cc_start: 0.7685 (mmt180) cc_final: 0.7031 (ptt90) REVERT: B 635 GLU cc_start: 0.8260 (tp30) cc_final: 0.7903 (tp30) REVERT: C 254 GLU cc_start: 0.2702 (OUTLIER) cc_final: 0.2111 (mt-10) REVERT: D 160 MET cc_start: 0.7851 (ppp) cc_final: 0.7622 (ppp) REVERT: D 220 ASN cc_start: 0.7795 (m-40) cc_final: 0.7591 (m110) REVERT: D 258 MET cc_start: 0.3915 (mtt) cc_final: 0.2537 (ttm) REVERT: D 372 MET cc_start: 0.7885 (ptp) cc_final: 0.7517 (ptp) REVERT: D 427 MET cc_start: 0.8297 (mmm) cc_final: 0.7286 (tmm) REVERT: D 439 MET cc_start: 0.9451 (ppp) cc_final: 0.9159 (ppp) REVERT: D 552 ARG cc_start: 0.7495 (mmm160) cc_final: 0.5528 (mmp80) REVERT: E 85 MET cc_start: 0.1260 (tpt) cc_final: 0.0705 (ptt) REVERT: E 276 MET cc_start: 0.8073 (mpp) cc_final: 0.7705 (mpp) REVERT: E 351 LEU cc_start: 0.8744 (tp) cc_final: 0.8467 (mt) REVERT: E 401 MET cc_start: 0.8629 (mmm) cc_final: 0.7937 (ppp) REVERT: E 439 MET cc_start: 0.8858 (mmm) cc_final: 0.8630 (mmm) REVERT: E 683 MET cc_start: 0.5541 (OUTLIER) cc_final: 0.5083 (mtp) REVERT: E 713 MET cc_start: 0.6448 (ppp) cc_final: 0.6117 (ppp) REVERT: F 328 ARG cc_start: 0.7903 (mpt180) cc_final: 0.7367 (tpt90) REVERT: F 427 MET cc_start: 0.6524 (tpt) cc_final: 0.6231 (tpt) REVERT: F 475 GLN cc_start: 0.7957 (mp10) cc_final: 0.7594 (mp10) REVERT: F 496 MET cc_start: 0.6314 (pmm) cc_final: 0.5332 (pmm) REVERT: F 583 TYR cc_start: 0.7588 (m-80) cc_final: 0.7319 (m-10) outliers start: 102 outliers final: 90 residues processed: 307 average time/residue: 0.4886 time to fit residues: 248.2388 Evaluate side-chains 330 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 235 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 332 TYR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 454 HIS Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 225 TYR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 0.9980 chunk 390 optimal weight: 50.0000 chunk 112 optimal weight: 10.0000 chunk 337 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 367 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 376 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.113948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.080344 restraints weight = 138372.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.077183 restraints weight = 185920.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.076619 restraints weight = 216229.039| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 37128 Z= 0.332 Angle : 0.809 55.201 50324 Z= 0.427 Chirality : 0.049 0.781 5736 Planarity : 0.005 0.067 6548 Dihedral : 6.607 109.239 5142 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 33.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.44 % Allowed : 16.64 % Favored : 80.92 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.63 (0.12), residues: 4626 helix: -0.21 (0.11), residues: 1950 sheet: -2.06 (0.22), residues: 532 loop : -1.58 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 602 HIS 0.008 0.001 HIS E 666 PHE 0.028 0.002 PHE C 451 TYR 0.026 0.002 TYR D 225 ARG 0.022 0.000 ARG B 697 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6850.36 seconds wall clock time: 126 minutes 0.39 seconds (7560.39 seconds total)