Starting phenix.real_space_refine on Sat Sep 28 08:29:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/09_2024/6d7s_7824.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/09_2024/6d7s_7824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/09_2024/6d7s_7824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/09_2024/6d7s_7824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/09_2024/6d7s_7824.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/09_2024/6d7s_7824.cif" } resolution = 4.34 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= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12280 2.51 5 N 3218 2.21 5 O 3364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19018 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "B" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4753 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Unresolved chain links: 2 Chain breaks: 1 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Time building chain proxies: 10.73, per 1000 atoms: 0.56 Number of scatterers: 19018 At special positions: 0 Unit cell: (136.22, 136.22, 121.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3364 8.00 N 3218 7.00 C 12280 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 2.5 seconds 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 8 sheets defined 62.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.609A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.559A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.739A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.737A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 removed outlier: 3.794A pdb=" N THR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.562A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.605A pdb=" N ARG A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.925A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.602A pdb=" N LEU A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.819A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.608A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.559A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.740A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 342 removed outlier: 3.556A pdb=" N ILE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 346 No H-bonds generated for 'chain 'B' and resid 345 through 346' Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 removed outlier: 3.795A pdb=" N THR B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.562A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 removed outlier: 3.605A pdb=" N ARG B 470 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 4.381A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.924A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.602A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 3.820A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.609A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.560A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.683A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.567A pdb=" N PHE C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.740A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 445 removed outlier: 3.794A pdb=" N THR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.561A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.604A pdb=" N ARG C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.924A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.345A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.603A pdb=" N LEU C 530 " --> pdb=" O TYR C 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 3.819A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.608A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.560A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.579A pdb=" N ALA D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.562A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE D 152 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.929A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.739A pdb=" N LEU D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.537A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 removed outlier: 4.288A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.566A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 445 removed outlier: 3.795A pdb=" N THR D 431 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.561A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 472 removed outlier: 3.604A pdb=" N ARG D 470 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.925A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.603A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 removed outlier: 3.820A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 587 removed outlier: 3.627A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA6, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.843A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'D' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6085 1.34 - 1.46: 4458 1.46 - 1.58: 8641 1.58 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 19448 Sorted by residual: bond pdb=" C GLU C 164 " pdb=" N HIS C 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.42e+00 bond pdb=" C GLU A 164 " pdb=" N HIS A 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.34e+00 bond pdb=" C GLU B 164 " pdb=" N HIS B 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.32e+00 bond pdb=" C GLU D 164 " pdb=" N HIS D 165 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.27e+00 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.83e+00 ... (remaining 19443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 26008 3.67 - 7.35: 310 7.35 - 11.02: 64 11.02 - 14.70: 0 14.70 - 18.37: 4 Bond angle restraints: 26386 Sorted by residual: angle pdb=" C ASP D 223 " pdb=" N ARG D 224 " pdb=" CA ARG D 224 " ideal model delta sigma weight residual 120.54 129.35 -8.81 1.35e+00 5.49e-01 4.26e+01 angle pdb=" C ASP A 223 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " ideal model delta sigma weight residual 120.54 129.33 -8.79 1.35e+00 5.49e-01 4.24e+01 angle pdb=" C ASP C 223 " pdb=" N ARG C 224 " pdb=" CA ARG C 224 " ideal model delta sigma weight residual 120.54 129.31 -8.77 1.35e+00 5.49e-01 4.22e+01 angle pdb=" C ASP B 223 " pdb=" N ARG B 224 " pdb=" CA ARG B 224 " ideal model delta sigma weight residual 120.54 129.29 -8.75 1.35e+00 5.49e-01 4.20e+01 angle pdb=" N LEU D 612 " pdb=" CA LEU D 612 " pdb=" C LEU D 612 " ideal model delta sigma weight residual 114.56 106.46 8.10 1.27e+00 6.20e-01 4.06e+01 ... (remaining 26381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 10916 16.66 - 33.33: 584 33.33 - 49.99: 132 49.99 - 66.66: 8 66.66 - 83.32: 28 Dihedral angle restraints: 11668 sinusoidal: 4718 harmonic: 6950 Sorted by residual: dihedral pdb=" CA SER B 291 " pdb=" C SER B 291 " pdb=" N LEU B 292 " pdb=" CA LEU B 292 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER A 291 " pdb=" C SER A 291 " pdb=" N LEU A 292 " pdb=" CA LEU A 292 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER D 291 " pdb=" C SER D 291 " pdb=" N LEU D 292 " pdb=" CA LEU D 292 " ideal model delta harmonic sigma weight residual 180.00 150.87 29.13 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 11665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2189 0.057 - 0.114: 703 0.114 - 0.171: 94 0.171 - 0.228: 20 0.228 - 0.285: 4 Chirality restraints: 3010 Sorted by residual: chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3007 not shown) Planarity restraints: 3330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 353 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 353 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 354 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 353 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 354 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 354 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 354 " -0.036 5.00e-02 4.00e+02 ... (remaining 3327 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4620 2.78 - 3.31: 18427 3.31 - 3.84: 30816 3.84 - 4.37: 36892 4.37 - 4.90: 58694 Nonbonded interactions: 149449 Sorted by model distance: nonbonded pdb=" OD2 ASP B 279 " pdb=" OG1 THR B 281 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP C 279 " pdb=" OG1 THR C 281 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP A 279 " pdb=" OG1 THR A 281 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP D 279 " pdb=" OG1 THR D 281 " model vdw 2.249 3.040 nonbonded pdb=" O ARG B 443 " pdb=" OG SER B 446 " model vdw 2.295 3.040 ... (remaining 149444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) selection = chain 'B' selection = (chain 'C' and (resid 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) selection = (chain 'D' and (resid 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.630 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 0.077 19448 Z= 0.460 Angle : 1.160 18.370 26386 Z= 0.640 Chirality : 0.056 0.285 3010 Planarity : 0.007 0.064 3330 Dihedral : 11.857 83.321 7168 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.07 % Favored : 87.76 % Rotamer: Outliers : 1.17 % Allowed : 2.33 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.61 (0.12), residues: 2353 helix: -3.58 (0.08), residues: 1298 sheet: -5.34 (0.26), residues: 40 loop : -3.75 (0.16), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 593 HIS 0.018 0.003 HIS C 522 PHE 0.034 0.003 PHE D 162 TYR 0.021 0.003 TYR A 524 ARG 0.007 0.001 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 717 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. 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 63 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8094 (tptp) REVERT: A 92 LEU cc_start: 0.8365 (tp) cc_final: 0.7542 (tt) REVERT: A 200 LEU cc_start: 0.9531 (mt) cc_final: 0.9278 (mt) REVERT: A 245 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8926 (tttt) REVERT: A 294 GLU cc_start: 0.8950 (tt0) cc_final: 0.8399 (pt0) REVERT: A 464 ASN cc_start: 0.8532 (t160) cc_final: 0.8208 (t160) REVERT: A 466 MET cc_start: 0.9212 (mmt) cc_final: 0.8840 (mmm) REVERT: A 475 LEU cc_start: 0.8907 (mp) cc_final: 0.8321 (tt) REVERT: A 485 MET cc_start: 0.9056 (mmp) cc_final: 0.8582 (mmp) REVERT: A 491 MET cc_start: 0.7738 (mmm) cc_final: 0.6913 (tpt) REVERT: A 578 MET cc_start: 0.9095 (mmt) cc_final: 0.8845 (mmt) REVERT: A 580 ASP cc_start: 0.9071 (t0) cc_final: 0.8669 (t0) REVERT: A 590 ASP cc_start: 0.8145 (p0) cc_final: 0.7928 (p0) REVERT: A 591 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8634 (mp0) REVERT: B 36 GLN cc_start: 0.7605 (tm130) cc_final: 0.7242 (tm-30) REVERT: B 63 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8155 (tptp) REVERT: B 92 LEU cc_start: 0.8353 (tp) cc_final: 0.6391 (tt) REVERT: B 245 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8890 (mttt) REVERT: B 280 LEU cc_start: 0.8969 (tp) cc_final: 0.8669 (tp) REVERT: B 389 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7264 (tp30) REVERT: B 455 SER cc_start: 0.9351 (m) cc_final: 0.9126 (p) REVERT: B 463 CYS cc_start: 0.8989 (m) cc_final: 0.8461 (t) REVERT: B 491 MET cc_start: 0.7778 (mmm) cc_final: 0.7118 (tpt) REVERT: B 508 PHE cc_start: 0.9134 (m-10) cc_final: 0.8741 (m-80) REVERT: B 520 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8672 (tp) REVERT: B 535 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 580 ASP cc_start: 0.8811 (t0) cc_final: 0.8609 (t0) REVERT: C 63 LYS cc_start: 0.8538 (ttpp) cc_final: 0.7677 (tptp) REVERT: C 92 LEU cc_start: 0.8599 (tp) cc_final: 0.8280 (pt) REVERT: C 130 MET cc_start: 0.6892 (tpp) cc_final: 0.6469 (tpp) REVERT: C 160 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8200 (pt) REVERT: C 209 LYS cc_start: 0.8453 (mttp) cc_final: 0.8079 (ptpt) REVERT: C 245 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8507 (tttt) REVERT: C 400 LEU cc_start: 0.9075 (mt) cc_final: 0.8367 (tt) REVERT: C 464 ASN cc_start: 0.8694 (t160) cc_final: 0.8383 (t0) REVERT: C 466 MET cc_start: 0.8944 (mmt) cc_final: 0.8511 (mmm) REVERT: C 485 MET cc_start: 0.8937 (mmp) cc_final: 0.8144 (mmp) REVERT: C 512 PHE cc_start: 0.8804 (m-10) cc_final: 0.8590 (m-80) REVERT: C 515 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7794 (tp30) REVERT: C 559 TYR cc_start: 0.8959 (t80) cc_final: 0.8610 (t80) REVERT: C 607 LYS cc_start: 0.8838 (mttp) cc_final: 0.8280 (mmmt) REVERT: D 63 LYS cc_start: 0.8510 (ttpp) cc_final: 0.7706 (tptp) REVERT: D 92 LEU cc_start: 0.8513 (tp) cc_final: 0.6755 (tt) REVERT: D 309 ASP cc_start: 0.8664 (m-30) cc_final: 0.8231 (m-30) REVERT: D 466 MET cc_start: 0.9266 (mmt) cc_final: 0.8624 (mmm) REVERT: D 485 MET cc_start: 0.8903 (mmp) cc_final: 0.8483 (mmp) REVERT: D 491 MET cc_start: 0.7280 (mmm) cc_final: 0.6855 (tpp) REVERT: D 591 GLU cc_start: 0.8943 (mt-10) cc_final: 0.7983 (mm-30) outliers start: 24 outliers final: 8 residues processed: 739 average time/residue: 0.3139 time to fit residues: 348.1948 Evaluate side-chains 452 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 442 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 184 optimal weight: 0.0030 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 217 ASN A 267 GLN A 483 GLN A 596 GLN B 73 HIS B 165 HIS B 217 ASN B 267 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 165 HIS C 217 ASN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 357 ASN C 548 ASN D 73 HIS D 118 GLN D 165 HIS D 217 ASN D 267 GLN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 464 ASN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19448 Z= 0.229 Angle : 0.776 13.418 26386 Z= 0.393 Chirality : 0.043 0.233 3010 Planarity : 0.005 0.053 3330 Dihedral : 6.488 28.194 2590 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 0.44 % Allowed : 3.55 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.15), residues: 2353 helix: -1.34 (0.12), residues: 1314 sheet: -5.27 (0.16), residues: 56 loop : -3.35 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 29 HIS 0.006 0.001 HIS C 426 PHE 0.027 0.002 PHE D 434 TYR 0.014 0.001 TYR A 559 ARG 0.007 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 562 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8461 (ttpp) cc_final: 0.8194 (tptp) REVERT: A 65 LEU cc_start: 0.8295 (mp) cc_final: 0.7964 (mp) REVERT: A 78 MET cc_start: 0.4864 (ptt) cc_final: 0.4410 (ptt) REVERT: A 130 MET cc_start: 0.7243 (tpp) cc_final: 0.6930 (mmt) REVERT: A 181 LEU cc_start: 0.9301 (mm) cc_final: 0.9083 (tp) REVERT: A 215 MET cc_start: 0.8483 (mpp) cc_final: 0.8227 (mpp) REVERT: A 245 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8796 (tttt) REVERT: A 294 GLU cc_start: 0.8505 (tt0) cc_final: 0.8253 (pt0) REVERT: A 330 CYS cc_start: 0.9114 (m) cc_final: 0.8807 (m) REVERT: A 339 TYR cc_start: 0.9135 (t80) cc_final: 0.8590 (t80) REVERT: A 464 ASN cc_start: 0.8434 (t0) cc_final: 0.8150 (t0) REVERT: A 466 MET cc_start: 0.9244 (mmt) cc_final: 0.9033 (mmm) REVERT: A 485 MET cc_start: 0.9319 (mmp) cc_final: 0.8666 (mmp) REVERT: A 493 PHE cc_start: 0.8950 (t80) cc_final: 0.8743 (t80) REVERT: A 578 MET cc_start: 0.9253 (mmt) cc_final: 0.8865 (mmt) REVERT: A 580 ASP cc_start: 0.9329 (t0) cc_final: 0.9008 (t0) REVERT: A 602 VAL cc_start: 0.9331 (m) cc_final: 0.9121 (p) REVERT: B 29 TRP cc_start: 0.7525 (p90) cc_final: 0.7173 (p90) REVERT: B 63 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8252 (tptp) REVERT: B 65 LEU cc_start: 0.8307 (mp) cc_final: 0.8030 (mp) REVERT: B 92 LEU cc_start: 0.8404 (tp) cc_final: 0.7529 (tt) REVERT: B 127 ASN cc_start: 0.8421 (m110) cc_final: 0.7282 (p0) REVERT: B 132 LEU cc_start: 0.9127 (mt) cc_final: 0.8901 (mt) REVERT: B 245 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8711 (mttt) REVERT: B 389 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7395 (tp30) REVERT: B 464 ASN cc_start: 0.8580 (t0) cc_final: 0.8326 (t0) REVERT: B 474 MET cc_start: 0.7186 (ptt) cc_final: 0.6775 (ptt) REVERT: B 478 PHE cc_start: 0.8582 (m-80) cc_final: 0.8379 (m-10) REVERT: B 481 MET cc_start: 0.8778 (mtp) cc_final: 0.8353 (mtm) REVERT: B 491 MET cc_start: 0.8040 (mmm) cc_final: 0.7312 (tpt) REVERT: B 535 GLU cc_start: 0.8635 (mt-10) cc_final: 0.7343 (mt-10) REVERT: B 580 ASP cc_start: 0.8944 (t0) cc_final: 0.8732 (t0) REVERT: C 63 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7801 (tptp) REVERT: C 215 MET cc_start: 0.8275 (mpp) cc_final: 0.8022 (mpp) REVERT: C 232 LEU cc_start: 0.8727 (tp) cc_final: 0.8442 (tp) REVERT: C 245 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8362 (mttt) REVERT: C 400 LEU cc_start: 0.9212 (mt) cc_final: 0.8497 (tt) REVERT: C 428 LEU cc_start: 0.9494 (mp) cc_final: 0.9230 (mm) REVERT: C 464 ASN cc_start: 0.8854 (t0) cc_final: 0.8260 (t0) REVERT: C 466 MET cc_start: 0.9240 (mmt) cc_final: 0.8872 (mmm) REVERT: C 475 LEU cc_start: 0.9164 (tp) cc_final: 0.8835 (tp) REVERT: C 559 TYR cc_start: 0.9051 (t80) cc_final: 0.8384 (t80) REVERT: C 591 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8118 (tm-30) REVERT: C 607 LYS cc_start: 0.8953 (mttp) cc_final: 0.8450 (mmmt) REVERT: D 63 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7889 (tptp) REVERT: D 65 LEU cc_start: 0.8296 (mp) cc_final: 0.8044 (mp) REVERT: D 78 MET cc_start: 0.5203 (ptt) cc_final: 0.4714 (ptt) REVERT: D 92 LEU cc_start: 0.8283 (tp) cc_final: 0.7989 (tt) REVERT: D 245 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8882 (tttt) REVERT: D 307 ILE cc_start: 0.9556 (mm) cc_final: 0.9335 (mm) REVERT: D 339 TYR cc_start: 0.9107 (t80) cc_final: 0.8610 (t80) REVERT: D 435 MET cc_start: 0.9225 (mmp) cc_final: 0.8930 (mmp) REVERT: D 442 MET cc_start: 0.8278 (ttm) cc_final: 0.8075 (ttm) REVERT: D 578 MET cc_start: 0.9245 (mmt) cc_final: 0.8698 (mmt) REVERT: D 591 GLU cc_start: 0.8745 (mt-10) cc_final: 0.7765 (mm-30) outliers start: 9 outliers final: 2 residues processed: 567 average time/residue: 0.2723 time to fit residues: 240.4262 Evaluate side-chains 397 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 395 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 206 GLN A 290 GLN B 206 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 464 ASN B 513 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN D 290 GLN D 572 ASN D 596 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19448 Z= 0.293 Angle : 0.774 13.424 26386 Z= 0.393 Chirality : 0.044 0.190 3010 Planarity : 0.005 0.050 3330 Dihedral : 6.083 25.723 2590 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.19 % Allowed : 3.21 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.16), residues: 2353 helix: -0.32 (0.14), residues: 1320 sheet: -5.16 (0.19), residues: 56 loop : -3.20 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 321 HIS 0.005 0.001 HIS B 426 PHE 0.033 0.002 PHE A 425 TYR 0.017 0.002 TYR B 559 ARG 0.006 0.001 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 478 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. 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 63 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8160 (tptp) REVERT: A 66 LYS cc_start: 0.8001 (mppt) cc_final: 0.7587 (pptt) REVERT: A 78 MET cc_start: 0.4866 (ptt) cc_final: 0.4378 (ptt) REVERT: A 181 LEU cc_start: 0.9316 (mm) cc_final: 0.9097 (tp) REVERT: A 209 LYS cc_start: 0.8758 (mttt) cc_final: 0.8551 (mmtt) REVERT: A 245 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8634 (tttt) REVERT: A 330 CYS cc_start: 0.9241 (m) cc_final: 0.9018 (m) REVERT: A 339 TYR cc_start: 0.9094 (t80) cc_final: 0.8598 (t80) REVERT: A 450 GLU cc_start: 0.8484 (pt0) cc_final: 0.8177 (pt0) REVERT: A 463 CYS cc_start: 0.9073 (m) cc_final: 0.8609 (t) REVERT: A 464 ASN cc_start: 0.8855 (t0) cc_final: 0.8428 (t0) REVERT: A 466 MET cc_start: 0.9301 (mmt) cc_final: 0.9088 (mmm) REVERT: A 485 MET cc_start: 0.9372 (mmp) cc_final: 0.8540 (mmp) REVERT: A 501 ILE cc_start: 0.9548 (mm) cc_final: 0.9260 (tp) REVERT: A 506 SER cc_start: 0.9710 (m) cc_final: 0.9283 (p) REVERT: A 535 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 580 ASP cc_start: 0.9300 (t0) cc_final: 0.9031 (t0) REVERT: B 29 TRP cc_start: 0.7681 (p90) cc_final: 0.7376 (p90) REVERT: B 63 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8215 (tptp) REVERT: B 66 LYS cc_start: 0.7929 (mppt) cc_final: 0.7511 (pptt) REVERT: B 78 MET cc_start: 0.5312 (ptt) cc_final: 0.4986 (ptt) REVERT: B 92 LEU cc_start: 0.8503 (tp) cc_final: 0.7928 (tt) REVERT: B 209 LYS cc_start: 0.9145 (ptpt) cc_final: 0.8932 (mmtt) REVERT: B 232 LEU cc_start: 0.8952 (tp) cc_final: 0.8698 (tp) REVERT: B 245 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8602 (mttt) REVERT: B 389 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7602 (tp30) REVERT: B 464 ASN cc_start: 0.8880 (t0) cc_final: 0.8558 (t0) REVERT: B 475 LEU cc_start: 0.8974 (mp) cc_final: 0.8618 (tp) REVERT: B 491 MET cc_start: 0.7963 (mmm) cc_final: 0.7371 (tpt) REVERT: B 506 SER cc_start: 0.9645 (m) cc_final: 0.9244 (p) REVERT: B 535 GLU cc_start: 0.8695 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 580 ASP cc_start: 0.9076 (t0) cc_final: 0.8815 (t0) REVERT: C 63 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8071 (tptp) REVERT: C 78 MET cc_start: 0.5565 (ptt) cc_final: 0.5362 (ptt) REVERT: C 215 MET cc_start: 0.8311 (mpp) cc_final: 0.8061 (mpp) REVERT: C 245 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8440 (mttt) REVERT: C 330 CYS cc_start: 0.9121 (m) cc_final: 0.8902 (m) REVERT: C 428 LEU cc_start: 0.9557 (mp) cc_final: 0.9075 (mm) REVERT: C 464 ASN cc_start: 0.9060 (t0) cc_final: 0.8524 (t0) REVERT: C 466 MET cc_start: 0.9393 (mmt) cc_final: 0.9096 (mmm) REVERT: C 485 MET cc_start: 0.9101 (mmp) cc_final: 0.8102 (mmp) REVERT: C 491 MET cc_start: 0.8221 (tpt) cc_final: 0.7909 (tpp) REVERT: C 559 TYR cc_start: 0.9256 (t80) cc_final: 0.8634 (t80) REVERT: C 578 MET cc_start: 0.8770 (mmt) cc_final: 0.8542 (mmm) REVERT: C 591 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8228 (tm-30) REVERT: C 592 LEU cc_start: 0.9502 (mm) cc_final: 0.8758 (mm) REVERT: D 63 LYS cc_start: 0.8321 (ttpp) cc_final: 0.7932 (tptp) REVERT: D 78 MET cc_start: 0.5276 (ptt) cc_final: 0.4897 (ptt) REVERT: D 92 LEU cc_start: 0.8383 (tp) cc_final: 0.8170 (mt) REVERT: D 232 LEU cc_start: 0.8896 (tp) cc_final: 0.8689 (tp) REVERT: D 245 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8868 (tttt) REVERT: D 339 TYR cc_start: 0.9049 (t80) cc_final: 0.8545 (t80) REVERT: D 463 CYS cc_start: 0.9129 (m) cc_final: 0.8222 (t) REVERT: D 464 ASN cc_start: 0.8907 (t0) cc_final: 0.8051 (t0) REVERT: D 466 MET cc_start: 0.9221 (tpp) cc_final: 0.7582 (mpp) REVERT: D 559 TYR cc_start: 0.9477 (t80) cc_final: 0.9120 (t80) REVERT: D 578 MET cc_start: 0.9211 (mmt) cc_final: 0.8741 (mmm) REVERT: D 590 ASP cc_start: 0.8134 (p0) cc_final: 0.7668 (p0) REVERT: D 591 GLU cc_start: 0.8821 (mt-10) cc_final: 0.7838 (mm-30) outliers start: 4 outliers final: 1 residues processed: 482 average time/residue: 0.2780 time to fit residues: 208.9053 Evaluate side-chains 371 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 370 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 582 HIS ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN B 464 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN C 548 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19448 Z= 0.207 Angle : 0.706 13.669 26386 Z= 0.352 Chirality : 0.042 0.202 3010 Planarity : 0.004 0.054 3330 Dihedral : 5.703 26.355 2590 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.17), residues: 2353 helix: 0.19 (0.14), residues: 1315 sheet: -4.74 (0.24), residues: 56 loop : -3.20 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 593 HIS 0.003 0.001 HIS A 122 PHE 0.028 0.002 PHE C 523 TYR 0.014 0.001 TYR B 559 ARG 0.009 0.001 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. 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 34 ASP cc_start: 0.9034 (m-30) cc_final: 0.8461 (m-30) REVERT: A 63 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8279 (tptp) REVERT: A 209 LYS cc_start: 0.8730 (mttt) cc_final: 0.8422 (mttt) REVERT: A 245 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8701 (mttt) REVERT: A 339 TYR cc_start: 0.9137 (t80) cc_final: 0.8653 (t80) REVERT: A 466 MET cc_start: 0.9263 (mmt) cc_final: 0.9026 (mmm) REVERT: A 485 MET cc_start: 0.9252 (mmt) cc_final: 0.8561 (mmp) REVERT: A 506 SER cc_start: 0.9668 (m) cc_final: 0.9346 (p) REVERT: A 535 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8355 (mt-10) REVERT: A 541 ILE cc_start: 0.9490 (mm) cc_final: 0.9156 (mm) REVERT: A 580 ASP cc_start: 0.9190 (t0) cc_final: 0.8981 (t0) REVERT: A 590 ASP cc_start: 0.7821 (p0) cc_final: 0.7523 (p0) REVERT: A 591 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8327 (mp0) REVERT: B 29 TRP cc_start: 0.7692 (p90) cc_final: 0.7431 (p90) REVERT: B 63 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8329 (tptp) REVERT: B 209 LYS cc_start: 0.9096 (ptpt) cc_final: 0.8815 (mmtp) REVERT: B 232 LEU cc_start: 0.8908 (tp) cc_final: 0.8697 (tp) REVERT: B 245 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8758 (mttt) REVERT: B 339 TYR cc_start: 0.8742 (t80) cc_final: 0.8524 (t80) REVERT: B 389 GLU cc_start: 0.8798 (mt-10) cc_final: 0.7737 (tp30) REVERT: B 464 ASN cc_start: 0.8994 (t0) cc_final: 0.8719 (t0) REVERT: B 491 MET cc_start: 0.8060 (mmm) cc_final: 0.7785 (tpt) REVERT: B 497 MET cc_start: 0.7372 (ttp) cc_final: 0.7152 (ttp) REVERT: B 506 SER cc_start: 0.9660 (m) cc_final: 0.9296 (p) REVERT: B 535 GLU cc_start: 0.8707 (mt-10) cc_final: 0.7470 (mt-10) REVERT: B 577 MET cc_start: 0.8362 (ttm) cc_final: 0.7553 (ttm) REVERT: B 580 ASP cc_start: 0.8972 (t0) cc_final: 0.8747 (t0) REVERT: C 63 LYS cc_start: 0.8587 (ttpp) cc_final: 0.7996 (tptp) REVERT: C 215 MET cc_start: 0.8259 (mpp) cc_final: 0.8022 (mpp) REVERT: C 232 LEU cc_start: 0.8743 (tp) cc_final: 0.8534 (tp) REVERT: C 245 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8512 (mttt) REVERT: C 330 CYS cc_start: 0.9056 (m) cc_final: 0.7984 (p) REVERT: C 331 MET cc_start: 0.8172 (mtm) cc_final: 0.6446 (mmt) REVERT: C 339 TYR cc_start: 0.8809 (t80) cc_final: 0.8597 (t80) REVERT: C 428 LEU cc_start: 0.9412 (mp) cc_final: 0.9148 (mm) REVERT: C 464 ASN cc_start: 0.8974 (t0) cc_final: 0.8489 (t0) REVERT: C 466 MET cc_start: 0.9371 (mmt) cc_final: 0.9164 (mmm) REVERT: C 485 MET cc_start: 0.8917 (mmp) cc_final: 0.8614 (mmp) REVERT: C 491 MET cc_start: 0.8224 (tpt) cc_final: 0.7895 (tpp) REVERT: C 559 TYR cc_start: 0.9294 (t80) cc_final: 0.8930 (t80) REVERT: C 591 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8128 (tm-30) REVERT: C 592 LEU cc_start: 0.9524 (mm) cc_final: 0.8870 (mm) REVERT: D 63 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7943 (tptp) REVERT: D 245 LYS cc_start: 0.9094 (mtpt) cc_final: 0.8814 (mttt) REVERT: D 339 TYR cc_start: 0.9089 (t80) cc_final: 0.8737 (t80) REVERT: D 464 ASN cc_start: 0.8891 (t0) cc_final: 0.8413 (t0) REVERT: D 475 LEU cc_start: 0.8894 (tp) cc_final: 0.8694 (tp) REVERT: D 559 TYR cc_start: 0.9504 (t80) cc_final: 0.8898 (t80) REVERT: D 569 LEU cc_start: 0.9386 (tt) cc_final: 0.9101 (tt) REVERT: D 590 ASP cc_start: 0.7893 (p0) cc_final: 0.7518 (p0) REVERT: D 591 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7666 (mm-30) outliers start: 3 outliers final: 1 residues processed: 473 average time/residue: 0.2833 time to fit residues: 208.4076 Evaluate side-chains 363 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 362 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 0.0670 chunk 204 optimal weight: 0.0970 chunk 57 optimal weight: 20.0000 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN B 464 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS D 546 ASN D 596 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19448 Z= 0.173 Angle : 0.721 13.970 26386 Z= 0.351 Chirality : 0.043 0.272 3010 Planarity : 0.004 0.062 3330 Dihedral : 5.511 26.653 2590 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2353 helix: 0.37 (0.14), residues: 1324 sheet: -4.50 (0.28), residues: 56 loop : -3.19 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 29 HIS 0.013 0.001 HIS B 522 PHE 0.034 0.002 PHE D 434 TYR 0.011 0.001 TYR B 559 ARG 0.010 0.000 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. 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 63 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8137 (tptp) REVERT: A 66 LYS cc_start: 0.8098 (mppt) cc_final: 0.7608 (pptt) REVERT: A 182 LEU cc_start: 0.9493 (mm) cc_final: 0.9085 (mm) REVERT: A 245 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8661 (mttt) REVERT: A 339 TYR cc_start: 0.9133 (t80) cc_final: 0.8571 (t80) REVERT: A 485 MET cc_start: 0.9140 (mmp) cc_final: 0.8641 (mmp) REVERT: A 497 MET cc_start: 0.6796 (ttp) cc_final: 0.6561 (ttp) REVERT: A 506 SER cc_start: 0.9647 (m) cc_final: 0.9318 (p) REVERT: A 588 GLU cc_start: 0.7211 (mp0) cc_final: 0.6351 (mp0) REVERT: A 590 ASP cc_start: 0.7765 (p0) cc_final: 0.7428 (p0) REVERT: A 591 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8244 (mp0) REVERT: B 29 TRP cc_start: 0.7732 (p90) cc_final: 0.7450 (p90) REVERT: B 63 LYS cc_start: 0.8596 (ttpp) cc_final: 0.8276 (tptp) REVERT: B 66 LYS cc_start: 0.8091 (mppt) cc_final: 0.7557 (pptt) REVERT: B 200 LEU cc_start: 0.9261 (mt) cc_final: 0.8991 (mt) REVERT: B 245 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8610 (mttt) REVERT: B 389 GLU cc_start: 0.8764 (mt-10) cc_final: 0.7639 (tp30) REVERT: B 464 ASN cc_start: 0.8928 (t0) cc_final: 0.8707 (t0) REVERT: B 466 MET cc_start: 0.9156 (mmm) cc_final: 0.8782 (mmm) REVERT: B 474 MET cc_start: 0.6762 (ptt) cc_final: 0.6292 (ptt) REVERT: B 491 MET cc_start: 0.8035 (mmm) cc_final: 0.7711 (tpt) REVERT: B 497 MET cc_start: 0.7312 (ttp) cc_final: 0.6968 (ttp) REVERT: B 506 SER cc_start: 0.9654 (m) cc_final: 0.9292 (p) REVERT: B 535 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 577 MET cc_start: 0.8284 (ttm) cc_final: 0.7577 (ttm) REVERT: B 580 ASP cc_start: 0.8975 (t0) cc_final: 0.8718 (t0) REVERT: C 29 TRP cc_start: 0.7728 (p90) cc_final: 0.7483 (p90) REVERT: C 63 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8030 (tptp) REVERT: C 245 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8479 (mttt) REVERT: C 330 CYS cc_start: 0.9028 (m) cc_final: 0.7884 (p) REVERT: C 331 MET cc_start: 0.8004 (mtm) cc_final: 0.6346 (mmt) REVERT: C 339 TYR cc_start: 0.8814 (t80) cc_final: 0.8613 (t80) REVERT: C 464 ASN cc_start: 0.8968 (t0) cc_final: 0.8433 (t0) REVERT: C 485 MET cc_start: 0.8891 (mmp) cc_final: 0.8653 (mmp) REVERT: C 491 MET cc_start: 0.8190 (tpt) cc_final: 0.7906 (tpp) REVERT: C 492 ARG cc_start: 0.7947 (ptm-80) cc_final: 0.7568 (ptm160) REVERT: C 559 TYR cc_start: 0.9313 (t80) cc_final: 0.8931 (t80) REVERT: C 591 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8063 (tm-30) REVERT: C 592 LEU cc_start: 0.9505 (mm) cc_final: 0.8860 (mm) REVERT: D 63 LYS cc_start: 0.8422 (ttpp) cc_final: 0.7964 (tptp) REVERT: D 78 MET cc_start: 0.5471 (ttm) cc_final: 0.4620 (ptt) REVERT: D 110 MET cc_start: 0.8272 (mmm) cc_final: 0.7788 (mmm) REVERT: D 245 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8854 (mttt) REVERT: D 339 TYR cc_start: 0.9091 (t80) cc_final: 0.8734 (t80) REVERT: D 454 MET cc_start: 0.9075 (tpt) cc_final: 0.8864 (tpt) REVERT: D 464 ASN cc_start: 0.8769 (t0) cc_final: 0.8509 (t0) REVERT: D 485 MET cc_start: 0.8972 (mmp) cc_final: 0.8486 (mmp) REVERT: D 559 TYR cc_start: 0.9474 (t80) cc_final: 0.8666 (t80) REVERT: D 569 LEU cc_start: 0.9433 (tt) cc_final: 0.9194 (tt) REVERT: D 590 ASP cc_start: 0.7753 (p0) cc_final: 0.7452 (p0) REVERT: D 591 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7634 (mm-30) outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.2778 time to fit residues: 207.6685 Evaluate side-chains 368 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.9990 chunk 205 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19448 Z= 0.172 Angle : 0.709 14.282 26386 Z= 0.344 Chirality : 0.042 0.201 3010 Planarity : 0.004 0.048 3330 Dihedral : 5.335 26.038 2590 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2353 helix: 0.48 (0.14), residues: 1348 sheet: -4.20 (0.31), residues: 56 loop : -3.06 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 593 HIS 0.005 0.001 HIS B 522 PHE 0.041 0.002 PHE A 456 TYR 0.014 0.001 TYR B 339 ARG 0.011 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. 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 63 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8292 (tptp) REVERT: A 110 MET cc_start: 0.8089 (mmm) cc_final: 0.7715 (mmm) REVERT: A 245 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8599 (mttt) REVERT: A 255 MET cc_start: 0.8835 (tpp) cc_final: 0.8542 (tpp) REVERT: A 339 TYR cc_start: 0.9133 (t80) cc_final: 0.8634 (t80) REVERT: A 464 ASN cc_start: 0.8707 (t0) cc_final: 0.8383 (t0) REVERT: A 485 MET cc_start: 0.9154 (mmp) cc_final: 0.8655 (mmp) REVERT: A 535 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8430 (mt-10) REVERT: A 588 GLU cc_start: 0.7152 (mp0) cc_final: 0.6379 (mp0) REVERT: A 590 ASP cc_start: 0.7689 (p0) cc_final: 0.7322 (p0) REVERT: A 591 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8228 (mp0) REVERT: B 29 TRP cc_start: 0.7665 (p90) cc_final: 0.7398 (p90) REVERT: B 110 MET cc_start: 0.8244 (mmm) cc_final: 0.7797 (mmm) REVERT: B 200 LEU cc_start: 0.9275 (mt) cc_final: 0.9009 (mt) REVERT: B 245 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8574 (mttt) REVERT: B 330 CYS cc_start: 0.9291 (m) cc_final: 0.8928 (m) REVERT: B 345 MET cc_start: 0.8481 (mmp) cc_final: 0.8275 (mmm) REVERT: B 389 GLU cc_start: 0.8802 (mt-10) cc_final: 0.7777 (tp30) REVERT: B 464 ASN cc_start: 0.8922 (t160) cc_final: 0.8597 (t0) REVERT: B 491 MET cc_start: 0.8075 (mmm) cc_final: 0.7668 (tpp) REVERT: B 497 MET cc_start: 0.7391 (ttp) cc_final: 0.7178 (ttp) REVERT: B 506 SER cc_start: 0.9654 (m) cc_final: 0.9233 (p) REVERT: B 535 GLU cc_start: 0.8762 (mt-10) cc_final: 0.7200 (mt-10) REVERT: B 577 MET cc_start: 0.8285 (ttm) cc_final: 0.7633 (ttm) REVERT: B 580 ASP cc_start: 0.8921 (t0) cc_final: 0.8713 (t0) REVERT: B 590 ASP cc_start: 0.7625 (p0) cc_final: 0.7348 (p0) REVERT: B 591 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8277 (mp0) REVERT: C 29 TRP cc_start: 0.7717 (p90) cc_final: 0.7502 (p90) REVERT: C 63 LYS cc_start: 0.8631 (ttpp) cc_final: 0.8150 (tptp) REVERT: C 245 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8460 (mttt) REVERT: C 330 CYS cc_start: 0.8991 (m) cc_final: 0.7881 (t) REVERT: C 331 MET cc_start: 0.8031 (mtm) cc_final: 0.6516 (mmt) REVERT: C 339 TYR cc_start: 0.8790 (t80) cc_final: 0.8572 (t80) REVERT: C 464 ASN cc_start: 0.8806 (t0) cc_final: 0.8347 (t0) REVERT: C 491 MET cc_start: 0.8217 (tpt) cc_final: 0.7984 (tpp) REVERT: C 559 TYR cc_start: 0.9299 (t80) cc_final: 0.8788 (t80) REVERT: C 578 MET cc_start: 0.8884 (mmt) cc_final: 0.8416 (mmt) REVERT: C 591 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8043 (tm-30) REVERT: C 592 LEU cc_start: 0.9514 (mm) cc_final: 0.8906 (mm) REVERT: D 63 LYS cc_start: 0.8426 (ttpp) cc_final: 0.7976 (tptp) REVERT: D 110 MET cc_start: 0.8431 (mmm) cc_final: 0.7960 (mmm) REVERT: D 113 GLU cc_start: 0.8583 (tp30) cc_final: 0.8366 (tp30) REVERT: D 245 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8757 (tttt) REVERT: D 339 TYR cc_start: 0.9056 (t80) cc_final: 0.8698 (t80) REVERT: D 454 MET cc_start: 0.9239 (tpt) cc_final: 0.8865 (tpt) REVERT: D 466 MET cc_start: 0.9476 (mmt) cc_final: 0.9195 (tpp) REVERT: D 485 MET cc_start: 0.8967 (mmp) cc_final: 0.8459 (mmp) REVERT: D 559 TYR cc_start: 0.9476 (t80) cc_final: 0.9129 (t80) REVERT: D 569 LEU cc_start: 0.9450 (tt) cc_final: 0.9246 (tt) REVERT: D 580 ASP cc_start: 0.8675 (t70) cc_final: 0.8399 (t70) REVERT: D 590 ASP cc_start: 0.7683 (p0) cc_final: 0.7478 (p0) REVERT: D 591 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7686 (mm-30) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.2919 time to fit residues: 213.3500 Evaluate side-chains 376 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 130 optimal weight: 0.0040 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19448 Z= 0.166 Angle : 0.718 13.656 26386 Z= 0.347 Chirality : 0.042 0.267 3010 Planarity : 0.004 0.045 3330 Dihedral : 5.225 26.848 2590 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2353 helix: 0.54 (0.14), residues: 1353 sheet: -4.02 (0.33), residues: 56 loop : -3.09 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 593 HIS 0.005 0.001 HIS C 587 PHE 0.035 0.002 PHE D 434 TYR 0.010 0.001 TYR B 555 ARG 0.012 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 482 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7430 (p90) cc_final: 0.7105 (p90) REVERT: A 34 ASP cc_start: 0.8962 (m-30) cc_final: 0.8090 (m-30) REVERT: A 63 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8210 (tptp) REVERT: A 66 LYS cc_start: 0.8041 (mppt) cc_final: 0.7445 (pptt) REVERT: A 110 MET cc_start: 0.8198 (mmm) cc_final: 0.7846 (mmm) REVERT: A 245 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8587 (mttt) REVERT: A 339 TYR cc_start: 0.9133 (t80) cc_final: 0.8601 (t80) REVERT: A 464 ASN cc_start: 0.8660 (t0) cc_final: 0.8091 (t0) REVERT: A 485 MET cc_start: 0.9162 (mmp) cc_final: 0.8637 (mmp) REVERT: A 515 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8357 (tp30) REVERT: A 535 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 588 GLU cc_start: 0.7142 (mp0) cc_final: 0.6408 (mp0) REVERT: B 66 LYS cc_start: 0.8091 (mppt) cc_final: 0.7438 (pptt) REVERT: B 110 MET cc_start: 0.8045 (mmm) cc_final: 0.7810 (mmm) REVERT: B 200 LEU cc_start: 0.9264 (mt) cc_final: 0.8997 (mt) REVERT: B 209 LYS cc_start: 0.9099 (ptpt) cc_final: 0.8686 (mmtt) REVERT: B 245 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8592 (mttt) REVERT: B 330 CYS cc_start: 0.9226 (m) cc_final: 0.8207 (p) REVERT: B 339 TYR cc_start: 0.8907 (t80) cc_final: 0.8634 (t80) REVERT: B 389 GLU cc_start: 0.8846 (mt-10) cc_final: 0.7825 (tp30) REVERT: B 464 ASN cc_start: 0.8913 (t160) cc_final: 0.8684 (t0) REVERT: B 535 GLU cc_start: 0.8737 (mt-10) cc_final: 0.7133 (mt-10) REVERT: B 577 MET cc_start: 0.8167 (ttm) cc_final: 0.7477 (ttm) REVERT: B 580 ASP cc_start: 0.8921 (t0) cc_final: 0.8714 (t0) REVERT: B 591 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8387 (mp0) REVERT: C 29 TRP cc_start: 0.7716 (p90) cc_final: 0.7485 (p90) REVERT: C 63 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8060 (tptp) REVERT: C 200 LEU cc_start: 0.9113 (mt) cc_final: 0.8820 (mt) REVERT: C 245 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8482 (mttt) REVERT: C 330 CYS cc_start: 0.9000 (m) cc_final: 0.7877 (t) REVERT: C 331 MET cc_start: 0.8012 (mtm) cc_final: 0.6478 (mmt) REVERT: C 464 ASN cc_start: 0.8820 (t0) cc_final: 0.8364 (t0) REVERT: C 485 MET cc_start: 0.9049 (mmp) cc_final: 0.8095 (mmp) REVERT: C 489 ASP cc_start: 0.7764 (t0) cc_final: 0.7360 (t0) REVERT: C 491 MET cc_start: 0.8143 (tpt) cc_final: 0.7938 (tpp) REVERT: C 539 THR cc_start: 0.9547 (p) cc_final: 0.9339 (t) REVERT: C 559 TYR cc_start: 0.9313 (t80) cc_final: 0.8741 (t80) REVERT: C 578 MET cc_start: 0.8618 (mmt) cc_final: 0.8369 (mmt) REVERT: C 591 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7981 (tm-30) REVERT: C 592 LEU cc_start: 0.9491 (mm) cc_final: 0.8869 (mm) REVERT: D 34 ASP cc_start: 0.8977 (m-30) cc_final: 0.8361 (t70) REVERT: D 63 LYS cc_start: 0.8431 (ttpp) cc_final: 0.7934 (tptp) REVERT: D 213 CYS cc_start: 0.8465 (t) cc_final: 0.7998 (p) REVERT: D 245 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8534 (mttt) REVERT: D 339 TYR cc_start: 0.9067 (t80) cc_final: 0.8715 (t80) REVERT: D 464 ASN cc_start: 0.8801 (t0) cc_final: 0.8545 (t0) REVERT: D 466 MET cc_start: 0.9457 (mmt) cc_final: 0.9012 (mmm) REVERT: D 492 ARG cc_start: 0.8481 (ptm160) cc_final: 0.8236 (ptm-80) REVERT: D 559 TYR cc_start: 0.9455 (t80) cc_final: 0.9030 (t80) REVERT: D 569 LEU cc_start: 0.9415 (tt) cc_final: 0.9195 (tt) REVERT: D 580 ASP cc_start: 0.8681 (t70) cc_final: 0.8419 (t70) REVERT: D 591 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7666 (mm-30) outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.2813 time to fit residues: 210.1445 Evaluate side-chains 379 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 144 optimal weight: 0.0980 chunk 154 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 40 GLN A 513 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN D 548 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19448 Z= 0.195 Angle : 0.736 14.767 26386 Z= 0.357 Chirality : 0.043 0.249 3010 Planarity : 0.005 0.083 3330 Dihedral : 5.190 25.975 2590 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2353 helix: 0.55 (0.14), residues: 1372 sheet: -3.86 (0.33), residues: 56 loop : -2.96 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 593 HIS 0.005 0.001 HIS C 165 PHE 0.043 0.002 PHE A 456 TYR 0.014 0.001 TYR C 339 ARG 0.013 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 2.228 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7505 (p90) cc_final: 0.7183 (p90) REVERT: A 63 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8260 (tptp) REVERT: A 110 MET cc_start: 0.8195 (mmm) cc_final: 0.7907 (mmm) REVERT: A 245 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8578 (mttt) REVERT: A 339 TYR cc_start: 0.9155 (t80) cc_final: 0.8636 (t80) REVERT: A 454 MET cc_start: 0.9187 (tpt) cc_final: 0.8829 (tpt) REVERT: A 464 ASN cc_start: 0.8737 (t0) cc_final: 0.8355 (t0) REVERT: A 478 PHE cc_start: 0.8230 (m-10) cc_final: 0.7847 (m-10) REVERT: A 515 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8329 (tp30) REVERT: A 535 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8385 (mt-10) REVERT: A 559 TYR cc_start: 0.9364 (t80) cc_final: 0.9135 (t80) REVERT: B 110 MET cc_start: 0.8120 (mmm) cc_final: 0.7900 (mmm) REVERT: B 200 LEU cc_start: 0.9288 (mt) cc_final: 0.9025 (mt) REVERT: B 209 LYS cc_start: 0.9130 (ptpt) cc_final: 0.8703 (mmtt) REVERT: B 245 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8637 (mttt) REVERT: B 330 CYS cc_start: 0.9231 (m) cc_final: 0.8243 (p) REVERT: B 339 TYR cc_start: 0.8911 (t80) cc_final: 0.8660 (t80) REVERT: B 389 GLU cc_start: 0.8865 (mt-10) cc_final: 0.7863 (tp30) REVERT: B 464 ASN cc_start: 0.9005 (t160) cc_final: 0.8672 (t0) REVERT: B 481 MET cc_start: 0.8767 (mtp) cc_final: 0.8411 (tpp) REVERT: B 535 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 591 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8372 (mp0) REVERT: C 63 LYS cc_start: 0.8579 (ttpp) cc_final: 0.8109 (tptp) REVERT: C 110 MET cc_start: 0.8545 (mmm) cc_final: 0.8043 (mmm) REVERT: C 206 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8541 (mp10) REVERT: C 245 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8436 (mttt) REVERT: C 330 CYS cc_start: 0.9022 (m) cc_final: 0.7933 (t) REVERT: C 331 MET cc_start: 0.8104 (mtm) cc_final: 0.6565 (mmt) REVERT: C 464 ASN cc_start: 0.8832 (t0) cc_final: 0.8408 (t0) REVERT: C 474 MET cc_start: 0.6365 (ptt) cc_final: 0.6091 (ptt) REVERT: C 559 TYR cc_start: 0.9322 (t80) cc_final: 0.9056 (t80) REVERT: C 580 ASP cc_start: 0.8277 (t70) cc_final: 0.7967 (t70) REVERT: C 591 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8082 (tm-30) REVERT: C 596 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8295 (tp40) REVERT: D 29 TRP cc_start: 0.7581 (p90) cc_final: 0.7337 (p90) REVERT: D 63 LYS cc_start: 0.8456 (ttpp) cc_final: 0.7688 (tptp) REVERT: D 228 HIS cc_start: 0.7445 (m90) cc_final: 0.7202 (m90) REVERT: D 245 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8538 (mttt) REVERT: D 339 TYR cc_start: 0.9056 (t80) cc_final: 0.8684 (t80) REVERT: D 466 MET cc_start: 0.9499 (mmt) cc_final: 0.9264 (tpp) REVERT: D 485 MET cc_start: 0.9074 (mmp) cc_final: 0.8061 (mmp) REVERT: D 492 ARG cc_start: 0.8734 (ptm160) cc_final: 0.8170 (ptm160) REVERT: D 559 TYR cc_start: 0.9496 (t80) cc_final: 0.8928 (t80) REVERT: D 569 LEU cc_start: 0.9447 (tt) cc_final: 0.9220 (tt) REVERT: D 578 MET cc_start: 0.8666 (mmm) cc_final: 0.7518 (mmm) REVERT: D 580 ASP cc_start: 0.8610 (t70) cc_final: 0.8275 (t70) REVERT: D 591 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7725 (mm-30) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.2932 time to fit residues: 217.8464 Evaluate side-chains 366 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 211 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 118 GLN A 596 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19448 Z= 0.196 Angle : 0.751 14.490 26386 Z= 0.363 Chirality : 0.043 0.215 3010 Planarity : 0.004 0.066 3330 Dihedral : 5.149 25.744 2590 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2353 helix: 0.62 (0.14), residues: 1369 sheet: -3.66 (0.36), residues: 56 loop : -2.91 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 593 HIS 0.005 0.001 HIS B 426 PHE 0.041 0.002 PHE A 456 TYR 0.012 0.001 TYR C 339 ARG 0.014 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.135 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7553 (p90) cc_final: 0.7262 (p90) REVERT: A 63 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8203 (tptp) REVERT: A 66 LYS cc_start: 0.8037 (mppt) cc_final: 0.7485 (pptt) REVERT: A 110 MET cc_start: 0.8217 (mmm) cc_final: 0.7928 (mmm) REVERT: A 245 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8472 (mttt) REVERT: A 339 TYR cc_start: 0.9137 (t80) cc_final: 0.8734 (t80) REVERT: A 464 ASN cc_start: 0.8723 (t0) cc_final: 0.8217 (t0) REVERT: A 478 PHE cc_start: 0.8422 (m-10) cc_final: 0.8128 (m-10) REVERT: A 485 MET cc_start: 0.9158 (mmp) cc_final: 0.8138 (mmp) REVERT: A 515 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8374 (tp30) REVERT: A 535 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 559 TYR cc_start: 0.9365 (t80) cc_final: 0.9076 (t80) REVERT: A 578 MET cc_start: 0.9041 (mmm) cc_final: 0.7680 (mmm) REVERT: A 591 GLU cc_start: 0.8521 (pm20) cc_final: 0.8306 (pm20) REVERT: B 34 ASP cc_start: 0.8931 (m-30) cc_final: 0.8560 (m-30) REVERT: B 66 LYS cc_start: 0.8157 (mppt) cc_final: 0.7437 (pptt) REVERT: B 110 MET cc_start: 0.8196 (mmm) cc_final: 0.7867 (mmm) REVERT: B 200 LEU cc_start: 0.9289 (mt) cc_final: 0.9012 (mt) REVERT: B 209 LYS cc_start: 0.9142 (ptpt) cc_final: 0.8703 (mmtt) REVERT: B 330 CYS cc_start: 0.9215 (m) cc_final: 0.8215 (p) REVERT: B 339 TYR cc_start: 0.8958 (t80) cc_final: 0.8705 (t80) REVERT: B 389 GLU cc_start: 0.8879 (mt-10) cc_final: 0.7872 (tp30) REVERT: B 425 PHE cc_start: 0.7099 (p90) cc_final: 0.6716 (p90) REVERT: B 464 ASN cc_start: 0.9004 (t160) cc_final: 0.8740 (t0) REVERT: B 474 MET cc_start: 0.6572 (ptt) cc_final: 0.6150 (ptt) REVERT: B 530 LEU cc_start: 0.9517 (mp) cc_final: 0.9265 (mp) REVERT: B 535 GLU cc_start: 0.8751 (mt-10) cc_final: 0.7137 (mt-10) REVERT: B 591 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8360 (mp0) REVERT: B 607 LYS cc_start: 0.9030 (mttp) cc_final: 0.8762 (mttp) REVERT: C 63 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8089 (tptp) REVERT: C 110 MET cc_start: 0.8502 (mmm) cc_final: 0.8010 (mmm) REVERT: C 245 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8494 (mttt) REVERT: C 330 CYS cc_start: 0.9020 (m) cc_final: 0.8007 (t) REVERT: C 331 MET cc_start: 0.8077 (mtm) cc_final: 0.6579 (mmt) REVERT: C 464 ASN cc_start: 0.8836 (t0) cc_final: 0.8436 (t0) REVERT: C 559 TYR cc_start: 0.9337 (t80) cc_final: 0.8676 (t80) REVERT: C 591 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8076 (tm-30) REVERT: C 596 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8264 (tp40) REVERT: D 29 TRP cc_start: 0.7632 (p90) cc_final: 0.7428 (p90) REVERT: D 63 LYS cc_start: 0.8483 (ttpp) cc_final: 0.7661 (tptp) REVERT: D 206 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8480 (tt0) REVERT: D 245 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8473 (mttt) REVERT: D 339 TYR cc_start: 0.9057 (t80) cc_final: 0.8699 (t80) REVERT: D 429 ILE cc_start: 0.9095 (mm) cc_final: 0.8883 (mm) REVERT: D 466 MET cc_start: 0.9512 (mmt) cc_final: 0.9253 (tpp) REVERT: D 559 TYR cc_start: 0.9494 (t80) cc_final: 0.8857 (t80) REVERT: D 569 LEU cc_start: 0.9439 (tt) cc_final: 0.9145 (tt) REVERT: D 580 ASP cc_start: 0.8542 (t70) cc_final: 0.8257 (t70) REVERT: D 588 GLU cc_start: 0.6808 (mp0) cc_final: 0.5946 (mp0) REVERT: D 590 ASP cc_start: 0.7889 (p0) cc_final: 0.7629 (p0) REVERT: D 591 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8170 (mp0) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2800 time to fit residues: 199.6270 Evaluate side-chains 368 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 8.9990 chunk 106 optimal weight: 0.0470 chunk 155 optimal weight: 0.8980 chunk 235 optimal weight: 0.2980 chunk 216 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 118 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 596 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 206 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 548 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19448 Z= 0.172 Angle : 0.744 14.248 26386 Z= 0.356 Chirality : 0.042 0.197 3010 Planarity : 0.004 0.066 3330 Dihedral : 5.109 26.312 2590 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2353 helix: 0.65 (0.14), residues: 1370 sheet: -3.56 (0.38), residues: 56 loop : -2.86 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 593 HIS 0.010 0.001 HIS A 587 PHE 0.035 0.002 PHE A 456 TYR 0.010 0.001 TYR B 559 ARG 0.014 0.000 ARG A 606 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7566 (p90) cc_final: 0.7279 (p90) REVERT: A 63 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8198 (tptp) REVERT: A 66 LYS cc_start: 0.8035 (mppt) cc_final: 0.7493 (pptt) REVERT: A 110 MET cc_start: 0.8137 (mmm) cc_final: 0.7853 (mmm) REVERT: A 127 ASN cc_start: 0.8109 (m110) cc_final: 0.7175 (p0) REVERT: A 245 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8441 (mttt) REVERT: A 339 TYR cc_start: 0.9164 (t80) cc_final: 0.8674 (t80) REVERT: A 439 THR cc_start: 0.9096 (t) cc_final: 0.8826 (t) REVERT: A 454 MET cc_start: 0.9039 (tpt) cc_final: 0.8806 (tpt) REVERT: A 464 ASN cc_start: 0.8656 (t0) cc_final: 0.8260 (t0) REVERT: A 485 MET cc_start: 0.9163 (mmp) cc_final: 0.8138 (mmp) REVERT: A 515 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8391 (tp30) REVERT: A 528 MET cc_start: 0.8877 (ttm) cc_final: 0.8601 (ttm) REVERT: A 535 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8439 (mt-10) REVERT: A 578 MET cc_start: 0.8988 (mmm) cc_final: 0.7623 (mmm) REVERT: A 591 GLU cc_start: 0.8512 (pm20) cc_final: 0.8307 (pm20) REVERT: A 596 GLN cc_start: 0.8726 (tp40) cc_final: 0.7482 (tp40) REVERT: B 66 LYS cc_start: 0.8160 (mppt) cc_final: 0.7473 (pptt) REVERT: B 110 MET cc_start: 0.8084 (mmm) cc_final: 0.7853 (mmm) REVERT: B 200 LEU cc_start: 0.9264 (mt) cc_final: 0.9011 (mt) REVERT: B 209 LYS cc_start: 0.9112 (ptpt) cc_final: 0.8661 (mmtt) REVERT: B 245 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8629 (mttt) REVERT: B 330 CYS cc_start: 0.9158 (m) cc_final: 0.8115 (p) REVERT: B 339 TYR cc_start: 0.8978 (t80) cc_final: 0.8681 (t80) REVERT: B 389 GLU cc_start: 0.8928 (mt-10) cc_final: 0.7859 (tp30) REVERT: B 425 PHE cc_start: 0.7017 (p90) cc_final: 0.6666 (p90) REVERT: B 464 ASN cc_start: 0.8915 (t0) cc_final: 0.8503 (t0) REVERT: B 474 MET cc_start: 0.6429 (ptt) cc_final: 0.5887 (ptt) REVERT: B 485 MET cc_start: 0.9029 (mmp) cc_final: 0.8741 (mmp) REVERT: B 506 SER cc_start: 0.9332 (p) cc_final: 0.9045 (p) REVERT: B 528 MET cc_start: 0.8726 (ttm) cc_final: 0.8484 (ttm) REVERT: B 578 MET cc_start: 0.8812 (mmt) cc_final: 0.7480 (mmt) REVERT: B 591 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8359 (mp0) REVERT: B 607 LYS cc_start: 0.8971 (mttp) cc_final: 0.8765 (mttp) REVERT: C 63 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8077 (tptp) REVERT: C 110 MET cc_start: 0.8372 (mmm) cc_final: 0.8007 (mmm) REVERT: C 245 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8408 (mttt) REVERT: C 330 CYS cc_start: 0.8988 (m) cc_final: 0.7902 (t) REVERT: C 331 MET cc_start: 0.8062 (mtm) cc_final: 0.6514 (mmt) REVERT: C 464 ASN cc_start: 0.8866 (t0) cc_final: 0.8355 (t0) REVERT: C 485 MET cc_start: 0.8953 (mmp) cc_final: 0.7745 (mmp) REVERT: C 577 MET cc_start: 0.7976 (ttm) cc_final: 0.7676 (ttm) REVERT: C 578 MET cc_start: 0.8573 (mmm) cc_final: 0.7486 (mmm) REVERT: C 596 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8287 (tp40) REVERT: D 29 TRP cc_start: 0.7643 (p90) cc_final: 0.7422 (p90) REVERT: D 63 LYS cc_start: 0.8468 (ttpp) cc_final: 0.7854 (tptp) REVERT: D 78 MET cc_start: 0.4966 (tmm) cc_final: 0.3732 (ptp) REVERT: D 112 SER cc_start: 0.6711 (m) cc_final: 0.6181 (p) REVERT: D 206 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8439 (tt0) REVERT: D 220 LEU cc_start: 0.9243 (mm) cc_final: 0.9031 (pp) REVERT: D 245 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8425 (mttt) REVERT: D 339 TYR cc_start: 0.9058 (t80) cc_final: 0.8720 (t80) REVERT: D 466 MET cc_start: 0.9554 (mmt) cc_final: 0.9248 (tpp) REVERT: D 485 MET cc_start: 0.9230 (mmp) cc_final: 0.8243 (mmp) REVERT: D 528 MET cc_start: 0.8837 (ttm) cc_final: 0.8361 (ttm) REVERT: D 530 LEU cc_start: 0.9614 (mm) cc_final: 0.9233 (mm) REVERT: D 547 TYR cc_start: 0.8798 (m-10) cc_final: 0.8425 (m-10) REVERT: D 559 TYR cc_start: 0.9479 (t80) cc_final: 0.8887 (t80) REVERT: D 578 MET cc_start: 0.8749 (mmm) cc_final: 0.7647 (mmm) REVERT: D 580 ASP cc_start: 0.8422 (t70) cc_final: 0.8158 (t70) REVERT: D 590 ASP cc_start: 0.7733 (p0) cc_final: 0.7441 (p0) REVERT: D 591 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8182 (mp0) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.2763 time to fit residues: 206.6828 Evaluate side-chains 372 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 192 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 596 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076151 restraints weight = 66066.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078193 restraints weight = 39225.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079625 restraints weight = 26894.552| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19448 Z= 0.193 Angle : 0.742 14.213 26386 Z= 0.358 Chirality : 0.043 0.192 3010 Planarity : 0.004 0.071 3330 Dihedral : 5.127 26.163 2590 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2353 helix: 0.59 (0.14), residues: 1378 sheet: -3.19 (0.42), residues: 58 loop : -2.92 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 593 HIS 0.003 0.001 HIS C 228 PHE 0.036 0.002 PHE A 456 TYR 0.018 0.001 TYR C 559 ARG 0.009 0.000 ARG A 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4395.03 seconds wall clock time: 79 minutes 55.97 seconds (4795.97 seconds total)