Starting phenix.real_space_refine on Wed Apr 10 08:31:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/04_2024/6bo9_7121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/04_2024/6bo9_7121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/04_2024/6bo9_7121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/04_2024/6bo9_7121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/04_2024/6bo9_7121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo9_7121/04_2024/6bo9_7121.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 12304 2.51 5 N 3220 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "B" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Time building chain proxies: 9.63, per 1000 atoms: 0.51 Number of scatterers: 19048 At special positions: 0 Unit cell: (140.14, 140.14, 125.44, 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 3368 8.00 N 3220 7.00 C 12304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.37 Conformation dependent library (CDL) restraints added in 3.8 seconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 63.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.753A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.175A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 removed outlier: 4.105A pdb=" N ARG A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.860A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.717A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.725A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.032A 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: 3.846A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 removed outlier: 4.105A pdb=" N ARG B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.739A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.717A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.725A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.032A 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: 3.847A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.759A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.520A pdb=" N LEU B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.643A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 4.374A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.586A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 224 removed outlier: 4.104A pdb=" N ARG C 224 " --> pdb=" O SER C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.716A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.726A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.032A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 4.088A 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: 3.847A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.754A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN D 40 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.643A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 4.373A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.587A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 209 through 220 removed outlier: 4.174A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 224 removed outlier: 4.104A pdb=" N ARG D 224 " --> pdb=" O SER D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 224' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.716A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.624A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.738A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.861A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 446 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.716A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.726A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 493 through 512 removed outlier: 4.220A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.031A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 4.088A 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: 3.847A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.760A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.519A pdb=" N LEU D 573 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 960 hydrogen bonds defined for protein. 2760 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: 5.75 Time building geometry restraints manager: 7.73 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: 6070 1.34 - 1.46: 4285 1.46 - 1.58: 8865 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 19484 Sorted by residual: bond pdb=" C ILE A 565 " pdb=" N ALA A 566 " ideal model delta sigma weight residual 1.332 1.301 0.032 1.40e-02 5.10e+03 5.09e+00 bond pdb=" C ILE B 565 " pdb=" N ALA B 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.95e+00 bond pdb=" C ILE C 565 " pdb=" N ALA C 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.95e+00 bond pdb=" C ILE D 565 " pdb=" N ALA D 566 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" CA VAL D 404 " pdb=" CB VAL D 404 " ideal model delta sigma weight residual 1.534 1.548 -0.014 6.80e-03 2.16e+04 4.14e+00 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.33: 443 105.33 - 112.63: 10225 112.63 - 119.93: 7055 119.93 - 127.23: 8429 127.23 - 134.54: 288 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N SER B 112 " pdb=" CA SER B 112 " pdb=" C SER B 112 " ideal model delta sigma weight residual 108.79 117.21 -8.42 1.53e+00 4.27e-01 3.03e+01 angle pdb=" N SER C 112 " pdb=" CA SER C 112 " pdb=" C SER C 112 " ideal model delta sigma weight residual 108.79 117.17 -8.38 1.53e+00 4.27e-01 3.00e+01 angle pdb=" N SER A 112 " pdb=" CA SER A 112 " pdb=" C SER A 112 " ideal model delta sigma weight residual 108.79 117.16 -8.37 1.53e+00 4.27e-01 2.99e+01 angle pdb=" N SER D 112 " pdb=" CA SER D 112 " pdb=" C SER D 112 " ideal model delta sigma weight residual 108.79 117.14 -8.35 1.53e+00 4.27e-01 2.98e+01 angle pdb=" N LEU B 352 " pdb=" CA LEU B 352 " pdb=" C LEU B 352 " ideal model delta sigma weight residual 110.91 117.17 -6.26 1.17e+00 7.31e-01 2.86e+01 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 10904 15.36 - 30.73: 591 30.73 - 46.09: 177 46.09 - 61.45: 4 61.45 - 76.82: 12 Dihedral angle restraints: 11688 sinusoidal: 4728 harmonic: 6960 Sorted by residual: dihedral pdb=" CA ASN C 129 " pdb=" C ASN C 129 " pdb=" N MET C 130 " pdb=" CA MET C 130 " ideal model delta harmonic sigma weight residual 180.00 144.34 35.66 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA ASN D 129 " pdb=" C ASN D 129 " pdb=" N MET D 130 " pdb=" CA MET D 130 " ideal model delta harmonic sigma weight residual 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" CA ASN B 129 " pdb=" C ASN B 129 " pdb=" N MET B 130 " pdb=" CA MET B 130 " ideal model delta harmonic sigma weight residual 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 ... (remaining 11685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1969 0.049 - 0.097: 827 0.097 - 0.146: 168 0.146 - 0.195: 36 0.195 - 0.244: 12 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+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 2.28 0.24 2.00e-01 2.50e+01 1.46e+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 2.29 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3009 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 323 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ARG D 323 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG D 323 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR D 324 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 323 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ARG A 323 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG A 323 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 324 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 323 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ARG B 323 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG B 323 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR B 324 " -0.013 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 4393 2.78 - 3.31: 19040 3.31 - 3.84: 31753 3.84 - 4.37: 38142 4.37 - 4.90: 61257 Nonbonded interactions: 154585 Sorted by model distance: nonbonded pdb=" O VAL A 427 " pdb=" OG1 THR A 431 " model vdw 2.245 2.440 nonbonded pdb=" O VAL C 427 " pdb=" OG1 THR C 431 " model vdw 2.245 2.440 nonbonded pdb=" O VAL D 427 " pdb=" OG1 THR D 431 " model vdw 2.245 2.440 nonbonded pdb=" O VAL B 427 " pdb=" OG1 THR B 431 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR C 339 " pdb=" O THR C 392 " model vdw 2.259 2.440 ... (remaining 154580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.900 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 49.670 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 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 0.059 19484 Z= 0.428 Angle : 1.168 18.238 26440 Z= 0.658 Chirality : 0.055 0.244 3012 Planarity : 0.007 0.046 3336 Dihedral : 10.847 76.817 7184 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.97 % Allowed : 2.33 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.14), residues: 2356 helix: -2.49 (0.10), residues: 1348 sheet: -5.71 (0.21), residues: 56 loop : -3.13 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP C 593 HIS 0.017 0.002 HIS C 522 PHE 0.026 0.003 PHE B 425 TYR 0.024 0.003 TYR C 524 ARG 0.005 0.001 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 930 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7172 (ptpt) cc_final: 0.6900 (tppt) REVERT: A 160 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6449 (pp) REVERT: A 174 ASN cc_start: 0.6809 (t0) cc_final: 0.6135 (t0) REVERT: A 222 TYR cc_start: 0.8400 (m-80) cc_final: 0.7995 (m-80) REVERT: A 242 THR cc_start: 0.7231 (p) cc_final: 0.7027 (p) REVERT: A 246 LEU cc_start: 0.7454 (tp) cc_final: 0.6905 (tp) REVERT: A 259 LEU cc_start: 0.9054 (mp) cc_final: 0.8537 (mt) REVERT: A 279 ASP cc_start: 0.6636 (t70) cc_final: 0.6218 (t70) REVERT: A 281 THR cc_start: 0.7710 (m) cc_final: 0.7375 (p) REVERT: A 284 ASP cc_start: 0.7773 (t0) cc_final: 0.6751 (t0) REVERT: A 328 TYR cc_start: 0.6983 (m-10) cc_final: 0.6564 (m-10) REVERT: A 345 MET cc_start: 0.6098 (ttm) cc_final: 0.5610 (ttp) REVERT: A 382 ASP cc_start: 0.7672 (m-30) cc_final: 0.7206 (t0) REVERT: A 434 PHE cc_start: 0.7675 (m-80) cc_final: 0.7114 (t80) REVERT: A 442 MET cc_start: 0.8034 (tpp) cc_final: 0.7707 (ttp) REVERT: A 487 PHE cc_start: 0.7799 (m-80) cc_final: 0.7219 (m-10) REVERT: A 509 TYR cc_start: 0.7154 (t80) cc_final: 0.6793 (t80) REVERT: A 510 ILE cc_start: 0.6949 (mt) cc_final: 0.6533 (mt) REVERT: A 546 ASN cc_start: 0.8025 (t0) cc_final: 0.7712 (t0) REVERT: A 565 ILE cc_start: 0.6733 (tp) cc_final: 0.6144 (tp) REVERT: A 594 ARG cc_start: 0.7332 (ttm110) cc_final: 0.6879 (mtp-110) REVERT: A 630 PHE cc_start: 0.7926 (m-80) cc_final: 0.7579 (m-10) REVERT: B 71 LYS cc_start: 0.6775 (ptpt) cc_final: 0.6467 (tptm) REVERT: B 78 MET cc_start: 0.4439 (pmt) cc_final: 0.4206 (pmm) REVERT: B 110 MET cc_start: 0.6834 (mtp) cc_final: 0.6187 (mtp) REVERT: B 202 ILE cc_start: 0.8730 (mm) cc_final: 0.8463 (mm) REVERT: B 204 ILE cc_start: 0.8803 (mt) cc_final: 0.8599 (mt) REVERT: B 222 TYR cc_start: 0.8429 (m-80) cc_final: 0.7961 (m-80) REVERT: B 281 THR cc_start: 0.7751 (m) cc_final: 0.7356 (p) REVERT: B 294 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 354 PRO cc_start: 0.7496 (Cg_exo) cc_final: 0.7272 (Cg_endo) REVERT: B 440 MET cc_start: 0.7851 (tmm) cc_final: 0.7406 (tpp) REVERT: B 442 MET cc_start: 0.7843 (tpp) cc_final: 0.7516 (ttp) REVERT: B 450 GLU cc_start: 0.6742 (pt0) cc_final: 0.6214 (pt0) REVERT: B 460 LEU cc_start: 0.5272 (mp) cc_final: 0.4909 (mp) REVERT: B 491 MET cc_start: 0.6825 (mmm) cc_final: 0.6241 (ttp) REVERT: B 509 TYR cc_start: 0.6889 (t80) cc_final: 0.6429 (t80) REVERT: B 546 ASN cc_start: 0.8385 (t0) cc_final: 0.8012 (t0) REVERT: B 565 ILE cc_start: 0.6845 (tp) cc_final: 0.6242 (tp) REVERT: B 569 LEU cc_start: 0.5766 (tt) cc_final: 0.5316 (tt) REVERT: B 583 TRP cc_start: 0.6947 (t60) cc_final: 0.6491 (t60) REVERT: B 594 ARG cc_start: 0.7365 (ttm110) cc_final: 0.6829 (mtp-110) REVERT: B 630 PHE cc_start: 0.7855 (m-80) cc_final: 0.7302 (m-10) REVERT: C 71 LYS cc_start: 0.6985 (ptpt) cc_final: 0.6753 (tppt) REVERT: C 206 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8184 (mm-40) REVERT: C 222 TYR cc_start: 0.8431 (m-80) cc_final: 0.7894 (m-80) REVERT: C 242 THR cc_start: 0.7176 (p) cc_final: 0.6952 (t) REVERT: C 246 LEU cc_start: 0.7633 (tp) cc_final: 0.7224 (tp) REVERT: C 259 LEU cc_start: 0.9095 (mp) cc_final: 0.8832 (mt) REVERT: C 284 ASP cc_start: 0.7835 (t0) cc_final: 0.7433 (t0) REVERT: C 352 LEU cc_start: 0.7812 (mp) cc_final: 0.7265 (mm) REVERT: C 354 PRO cc_start: 0.8404 (Cg_exo) cc_final: 0.8165 (Cg_endo) REVERT: C 358 ASN cc_start: 0.7273 (p0) cc_final: 0.6938 (p0) REVERT: C 384 ILE cc_start: 0.8217 (mt) cc_final: 0.7958 (mp) REVERT: C 434 PHE cc_start: 0.7830 (m-80) cc_final: 0.7231 (t80) REVERT: C 487 PHE cc_start: 0.7909 (m-80) cc_final: 0.7630 (m-10) REVERT: C 491 MET cc_start: 0.6758 (mmm) cc_final: 0.6129 (ttp) REVERT: C 508 PHE cc_start: 0.6401 (m-10) cc_final: 0.6123 (m-10) REVERT: C 509 TYR cc_start: 0.6967 (t80) cc_final: 0.6525 (t80) REVERT: C 526 TYR cc_start: 0.7393 (t80) cc_final: 0.7013 (t80) REVERT: C 532 SER cc_start: 0.6967 (t) cc_final: 0.6661 (t) REVERT: C 546 ASN cc_start: 0.8170 (t0) cc_final: 0.7688 (t0) REVERT: C 565 ILE cc_start: 0.7008 (tp) cc_final: 0.6795 (tp) REVERT: C 569 LEU cc_start: 0.5979 (tt) cc_final: 0.5686 (tt) REVERT: C 583 TRP cc_start: 0.7082 (t60) cc_final: 0.6784 (t60) REVERT: C 594 ARG cc_start: 0.7353 (ttm110) cc_final: 0.6926 (mtp-110) REVERT: C 615 ARG cc_start: 0.6910 (mtm110) cc_final: 0.6568 (mtm110) REVERT: C 630 PHE cc_start: 0.8032 (m-80) cc_final: 0.7618 (m-80) REVERT: D 71 LYS cc_start: 0.6939 (ptpt) cc_final: 0.6607 (tptt) REVERT: D 110 MET cc_start: 0.6227 (mtp) cc_final: 0.5848 (mtp) REVERT: D 174 ASN cc_start: 0.6899 (t0) cc_final: 0.5609 (t0) REVERT: D 202 ILE cc_start: 0.8797 (mm) cc_final: 0.8519 (mm) REVERT: D 222 TYR cc_start: 0.8493 (m-80) cc_final: 0.7989 (m-80) REVERT: D 242 THR cc_start: 0.7084 (p) cc_final: 0.6869 (t) REVERT: D 246 LEU cc_start: 0.7459 (tp) cc_final: 0.7168 (tp) REVERT: D 259 LEU cc_start: 0.9077 (mp) cc_final: 0.8846 (tp) REVERT: D 264 LYS cc_start: 0.7971 (pttt) cc_final: 0.7693 (ptpp) REVERT: D 279 ASP cc_start: 0.6799 (t70) cc_final: 0.6153 (t70) REVERT: D 284 ASP cc_start: 0.7912 (t0) cc_final: 0.7178 (t0) REVERT: D 285 SER cc_start: 0.6453 (p) cc_final: 0.5994 (m) REVERT: D 323 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7600 (mtp180) REVERT: D 342 CYS cc_start: 0.8127 (t) cc_final: 0.7873 (t) REVERT: D 345 MET cc_start: 0.6383 (ttm) cc_final: 0.5965 (ttp) REVERT: D 352 LEU cc_start: 0.7886 (mp) cc_final: 0.7512 (mm) REVERT: D 390 LEU cc_start: 0.8877 (mt) cc_final: 0.8621 (tp) REVERT: D 434 PHE cc_start: 0.7753 (m-80) cc_final: 0.7100 (t80) REVERT: D 436 VAL cc_start: 0.7052 (t) cc_final: 0.6797 (m) REVERT: D 440 MET cc_start: 0.7989 (tmm) cc_final: 0.7241 (tpp) REVERT: D 453 PRO cc_start: 0.7524 (Cg_exo) cc_final: 0.7268 (Cg_endo) REVERT: D 491 MET cc_start: 0.7094 (mmm) cc_final: 0.6858 (ttp) REVERT: D 514 THR cc_start: 0.7948 (m) cc_final: 0.7642 (p) REVERT: D 522 HIS cc_start: 0.6402 (m-70) cc_final: 0.6011 (m170) REVERT: D 532 SER cc_start: 0.7199 (t) cc_final: 0.6864 (t) REVERT: D 534 PHE cc_start: 0.5598 (t80) cc_final: 0.5386 (t80) REVERT: D 546 ASN cc_start: 0.7900 (t0) cc_final: 0.7045 (t0) REVERT: D 594 ARG cc_start: 0.7246 (ttm110) cc_final: 0.6771 (mtp-110) REVERT: D 630 PHE cc_start: 0.8158 (m-80) cc_final: 0.7799 (m-10) outliers start: 20 outliers final: 2 residues processed: 942 average time/residue: 0.3290 time to fit residues: 459.7712 Evaluate side-chains 573 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 570 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 0.0670 chunk 112 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 214 optimal weight: 0.0870 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 HIS A 257 GLN A 357 ASN A 365 ASN A 464 ASN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 365 ASN B 522 HIS B 572 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 206 GLN C 257 GLN C 265 HIS C 267 GLN C 357 ASN C 365 ASN C 464 ASN C 522 HIS C 572 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 267 GLN D 464 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19484 Z= 0.202 Angle : 0.788 12.840 26440 Z= 0.384 Chirality : 0.044 0.231 3012 Planarity : 0.005 0.038 3336 Dihedral : 5.961 47.533 2600 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.51 % Favored : 90.45 % Rotamer: Outliers : 3.73 % Allowed : 15.21 % Favored : 81.06 % 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: -2.17 (0.16), residues: 2356 helix: -0.52 (0.13), residues: 1384 sheet: -4.68 (0.31), residues: 56 loop : -2.64 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 629 HIS 0.006 0.001 HIS A 185 PHE 0.031 0.002 PHE C 531 TYR 0.026 0.002 TYR A 270 ARG 0.006 0.001 ARG D 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 644 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7218 (ptpt) cc_final: 0.6965 (tppt) REVERT: A 218 LEU cc_start: 0.8674 (tp) cc_final: 0.8419 (tp) REVERT: A 222 TYR cc_start: 0.8230 (m-80) cc_final: 0.7984 (m-10) REVERT: A 241 LEU cc_start: 0.7980 (mm) cc_final: 0.7770 (mm) REVERT: A 255 MET cc_start: 0.8102 (tpp) cc_final: 0.7850 (mmm) REVERT: A 281 THR cc_start: 0.7580 (m) cc_final: 0.7348 (p) REVERT: A 345 MET cc_start: 0.5766 (ttm) cc_final: 0.5526 (ttp) REVERT: A 437 LEU cc_start: 0.8146 (mt) cc_final: 0.7930 (pp) REVERT: A 440 MET cc_start: 0.7135 (ppp) cc_final: 0.6876 (tpp) REVERT: A 456 PHE cc_start: 0.5693 (m-10) cc_final: 0.5367 (m-80) REVERT: A 464 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7701 (t0) REVERT: A 487 PHE cc_start: 0.7546 (m-80) cc_final: 0.7230 (m-80) REVERT: A 509 TYR cc_start: 0.7152 (t80) cc_final: 0.6850 (t80) REVERT: A 528 MET cc_start: 0.7256 (tmm) cc_final: 0.6977 (tmm) REVERT: A 534 PHE cc_start: 0.5528 (t80) cc_final: 0.5325 (t80) REVERT: A 546 ASN cc_start: 0.7871 (t0) cc_final: 0.7503 (t0) REVERT: A 577 MET cc_start: 0.7037 (mtm) cc_final: 0.6801 (mtm) REVERT: A 583 TRP cc_start: 0.7140 (t60) cc_final: 0.6630 (t60) REVERT: A 594 ARG cc_start: 0.7271 (ttm110) cc_final: 0.6951 (mtp180) REVERT: A 598 VAL cc_start: 0.7517 (t) cc_final: 0.7246 (m) REVERT: A 618 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6627 (tp) REVERT: B 31 GLN cc_start: 0.5759 (tt0) cc_final: 0.5538 (tp40) REVERT: B 71 LYS cc_start: 0.6912 (ptpt) cc_final: 0.6596 (tptm) REVERT: B 218 LEU cc_start: 0.8650 (tp) cc_final: 0.8372 (tp) REVERT: B 222 TYR cc_start: 0.8263 (m-80) cc_final: 0.8033 (m-10) REVERT: B 281 THR cc_start: 0.7873 (m) cc_final: 0.7564 (p) REVERT: B 328 TYR cc_start: 0.7135 (m-10) cc_final: 0.6468 (m-10) REVERT: B 345 MET cc_start: 0.7285 (mmp) cc_final: 0.6014 (ttp) REVERT: B 354 PRO cc_start: 0.7801 (Cg_exo) cc_final: 0.7582 (Cg_endo) REVERT: B 440 MET cc_start: 0.7605 (tmm) cc_final: 0.7275 (tpp) REVERT: B 491 MET cc_start: 0.6757 (mmm) cc_final: 0.6113 (ttp) REVERT: B 546 ASN cc_start: 0.8468 (t0) cc_final: 0.8027 (t0) REVERT: B 583 TRP cc_start: 0.7062 (t60) cc_final: 0.6709 (t60) REVERT: B 590 ASP cc_start: 0.7310 (m-30) cc_final: 0.7106 (t70) REVERT: B 618 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6653 (tp) REVERT: B 627 ASP cc_start: 0.8604 (t0) cc_final: 0.8189 (m-30) REVERT: C 45 TRP cc_start: 0.7152 (t-100) cc_final: 0.6845 (t-100) REVERT: C 71 LYS cc_start: 0.7074 (ptpt) cc_final: 0.6840 (tppt) REVERT: C 150 THR cc_start: 0.6604 (m) cc_final: 0.6132 (p) REVERT: C 184 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8483 (mt-10) REVERT: C 185 HIS cc_start: 0.6954 (m90) cc_final: 0.6730 (m90) REVERT: C 206 GLN cc_start: 0.8374 (mm110) cc_final: 0.8095 (mm-40) REVERT: C 218 LEU cc_start: 0.8737 (tp) cc_final: 0.8499 (tp) REVERT: C 222 TYR cc_start: 0.8308 (m-80) cc_final: 0.8030 (m-10) REVERT: C 282 GLU cc_start: 0.7851 (mp0) cc_final: 0.7596 (mp0) REVERT: C 345 MET cc_start: 0.7683 (mmm) cc_final: 0.6443 (ttt) REVERT: C 434 PHE cc_start: 0.7708 (m-80) cc_final: 0.7105 (t80) REVERT: C 463 CYS cc_start: 0.7491 (m) cc_final: 0.7215 (m) REVERT: C 464 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7686 (t0) REVERT: C 491 MET cc_start: 0.6603 (mmm) cc_final: 0.6145 (ttp) REVERT: C 509 TYR cc_start: 0.7117 (t80) cc_final: 0.6808 (t80) REVERT: C 514 THR cc_start: 0.7580 (m) cc_final: 0.7130 (p) REVERT: C 526 TYR cc_start: 0.7561 (t80) cc_final: 0.7259 (t80) REVERT: C 528 MET cc_start: 0.7701 (tmm) cc_final: 0.7444 (tmm) REVERT: C 546 ASN cc_start: 0.8238 (t0) cc_final: 0.7814 (t0) REVERT: C 565 ILE cc_start: 0.6907 (tp) cc_final: 0.6698 (tp) REVERT: C 583 TRP cc_start: 0.7106 (t60) cc_final: 0.6666 (t60) REVERT: C 594 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7098 (mtp-110) REVERT: C 629 TRP cc_start: 0.7053 (m-10) cc_final: 0.6626 (m-10) REVERT: D 71 LYS cc_start: 0.7028 (ptpt) cc_final: 0.6750 (tptt) REVERT: D 218 LEU cc_start: 0.8716 (tp) cc_final: 0.8187 (tt) REVERT: D 222 TYR cc_start: 0.8342 (m-80) cc_final: 0.7791 (m-80) REVERT: D 282 GLU cc_start: 0.7743 (mp0) cc_final: 0.7532 (mp0) REVERT: D 301 LYS cc_start: 0.7313 (mtpp) cc_final: 0.7070 (mtmt) REVERT: D 342 CYS cc_start: 0.8063 (t) cc_final: 0.7800 (t) REVERT: D 345 MET cc_start: 0.6218 (ttm) cc_final: 0.5947 (ttp) REVERT: D 390 LEU cc_start: 0.8832 (mt) cc_final: 0.8627 (tp) REVERT: D 434 PHE cc_start: 0.7651 (m-80) cc_final: 0.7086 (t80) REVERT: D 436 VAL cc_start: 0.6979 (t) cc_final: 0.6735 (m) REVERT: D 440 MET cc_start: 0.8030 (tmm) cc_final: 0.7303 (tpp) REVERT: D 450 GLU cc_start: 0.7762 (pt0) cc_final: 0.7550 (pm20) REVERT: D 453 PRO cc_start: 0.7820 (Cg_exo) cc_final: 0.7611 (Cg_endo) REVERT: D 528 MET cc_start: 0.7499 (tmm) cc_final: 0.7289 (tmm) REVERT: D 583 TRP cc_start: 0.7342 (t60) cc_final: 0.7100 (t60) REVERT: D 594 ARG cc_start: 0.7254 (ttm110) cc_final: 0.6987 (mtp-110) outliers start: 77 outliers final: 33 residues processed: 690 average time/residue: 0.3214 time to fit residues: 343.0683 Evaluate side-chains 568 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 531 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 464 ASN Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 511 ILE Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 619 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 214 optimal weight: 0.0010 chunk 231 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 overall best weight: 3.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 572 ASN ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 357 ASN B 464 ASN B 546 ASN C 31 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN D 546 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19484 Z= 0.327 Angle : 0.821 12.438 26440 Z= 0.405 Chirality : 0.047 0.265 3012 Planarity : 0.005 0.053 3336 Dihedral : 5.599 47.578 2598 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.99 % Allowed : 18.56 % Favored : 76.45 % 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: -1.13 (0.18), residues: 2356 helix: 0.41 (0.14), residues: 1372 sheet: -4.05 (0.35), residues: 56 loop : -2.33 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 29 HIS 0.006 0.001 HIS B 165 PHE 0.033 0.002 PHE B 531 TYR 0.024 0.002 TYR A 547 ARG 0.006 0.001 ARG C 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 567 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8704 (mt-10) REVERT: A 185 HIS cc_start: 0.7117 (m90) cc_final: 0.6874 (m90) REVERT: A 218 LEU cc_start: 0.8391 (tp) cc_final: 0.7820 (tp) REVERT: A 222 TYR cc_start: 0.8357 (m-80) cc_final: 0.7920 (m-80) REVERT: A 250 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7311 (tp30) REVERT: A 311 THR cc_start: 0.6234 (OUTLIER) cc_final: 0.5661 (p) REVERT: A 315 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7659 (mp0) REVERT: A 342 CYS cc_start: 0.8164 (t) cc_final: 0.7952 (t) REVERT: A 345 MET cc_start: 0.6169 (ttm) cc_final: 0.5956 (ttp) REVERT: A 352 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7227 (mm) REVERT: A 434 PHE cc_start: 0.7813 (m-80) cc_final: 0.7326 (t80) REVERT: A 436 VAL cc_start: 0.6819 (t) cc_final: 0.6557 (m) REVERT: A 440 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6896 (mmm) REVERT: A 463 CYS cc_start: 0.7084 (m) cc_final: 0.6880 (m) REVERT: A 487 PHE cc_start: 0.7434 (m-80) cc_final: 0.7159 (m-80) REVERT: A 528 MET cc_start: 0.7581 (tmm) cc_final: 0.7230 (tmm) REVERT: A 538 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6644 (mp) REVERT: A 546 ASN cc_start: 0.8025 (t0) cc_final: 0.7769 (t0) REVERT: A 577 MET cc_start: 0.6987 (mtm) cc_final: 0.6777 (mtp) REVERT: A 578 MET cc_start: 0.7754 (mtm) cc_final: 0.7546 (mtm) REVERT: A 583 TRP cc_start: 0.7259 (t60) cc_final: 0.6887 (t60) REVERT: A 591 GLU cc_start: 0.8122 (tt0) cc_final: 0.7417 (tm-30) REVERT: A 594 ARG cc_start: 0.7530 (ttm110) cc_final: 0.7118 (mtp-110) REVERT: A 618 ILE cc_start: 0.7395 (mm) cc_final: 0.7048 (tp) REVERT: B 71 LYS cc_start: 0.6812 (ptpt) cc_final: 0.6377 (tptt) REVERT: B 96 MET cc_start: 0.8385 (tmm) cc_final: 0.8108 (mtm) REVERT: B 130 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6966 (mmm) REVERT: B 218 LEU cc_start: 0.8446 (tp) cc_final: 0.8052 (tp) REVERT: B 222 TYR cc_start: 0.8310 (m-80) cc_final: 0.7905 (m-80) REVERT: B 228 HIS cc_start: 0.6267 (m-70) cc_final: 0.5123 (p-80) REVERT: B 281 THR cc_start: 0.7976 (m) cc_final: 0.7628 (p) REVERT: B 284 ASP cc_start: 0.8051 (t0) cc_final: 0.7801 (t0) REVERT: B 294 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7533 (mt-10) REVERT: B 339 TYR cc_start: 0.7213 (t80) cc_final: 0.6747 (t80) REVERT: B 342 CYS cc_start: 0.8116 (t) cc_final: 0.7853 (t) REVERT: B 345 MET cc_start: 0.7687 (mmp) cc_final: 0.6248 (ttt) REVERT: B 434 PHE cc_start: 0.7678 (m-80) cc_final: 0.7150 (t80) REVERT: B 440 MET cc_start: 0.7844 (tmm) cc_final: 0.7384 (tpp) REVERT: B 463 CYS cc_start: 0.7307 (m) cc_final: 0.7072 (m) REVERT: B 487 PHE cc_start: 0.7764 (m-80) cc_final: 0.7296 (m-80) REVERT: B 491 MET cc_start: 0.6785 (mmm) cc_final: 0.6464 (ttp) REVERT: B 546 ASN cc_start: 0.8309 (t0) cc_final: 0.8040 (t0) REVERT: B 557 ILE cc_start: 0.7572 (mm) cc_final: 0.7359 (mt) REVERT: B 567 THR cc_start: 0.6832 (m) cc_final: 0.6627 (m) REVERT: B 583 TRP cc_start: 0.7148 (t60) cc_final: 0.6819 (t60) REVERT: B 594 ARG cc_start: 0.6784 (mtm-85) cc_final: 0.6568 (mtp180) REVERT: B 629 TRP cc_start: 0.7009 (m-10) cc_final: 0.6795 (m-10) REVERT: C 54 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7784 (mmtm) REVERT: C 130 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6846 (tpp) REVERT: C 184 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8685 (mt-10) REVERT: C 185 HIS cc_start: 0.7030 (m90) cc_final: 0.6795 (m90) REVERT: C 218 LEU cc_start: 0.8376 (tp) cc_final: 0.7874 (tt) REVERT: C 222 TYR cc_start: 0.8418 (m-80) cc_final: 0.7839 (m-80) REVERT: C 228 HIS cc_start: 0.6412 (m-70) cc_final: 0.5221 (p-80) REVERT: C 250 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7229 (tm-30) REVERT: C 339 TYR cc_start: 0.6823 (t80) cc_final: 0.6618 (t80) REVERT: C 345 MET cc_start: 0.7903 (mmm) cc_final: 0.6673 (ttt) REVERT: C 434 PHE cc_start: 0.7851 (m-80) cc_final: 0.7258 (t80) REVERT: C 546 ASN cc_start: 0.8115 (t0) cc_final: 0.7859 (t0) REVERT: C 583 TRP cc_start: 0.7114 (t60) cc_final: 0.6752 (t60) REVERT: C 591 GLU cc_start: 0.8108 (tt0) cc_final: 0.7484 (tm-30) REVERT: C 594 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7066 (mtp-110) REVERT: C 616 SER cc_start: 0.8460 (t) cc_final: 0.7855 (p) REVERT: C 629 TRP cc_start: 0.7467 (m-10) cc_final: 0.6784 (m100) REVERT: D 118 GLN cc_start: 0.6638 (tm-30) cc_final: 0.6313 (tm-30) REVERT: D 222 TYR cc_start: 0.8407 (m-80) cc_final: 0.7848 (m-80) REVERT: D 282 GLU cc_start: 0.7499 (mp0) cc_final: 0.7162 (mp0) REVERT: D 315 GLU cc_start: 0.7798 (mp0) cc_final: 0.7583 (mp0) REVERT: D 324 TYR cc_start: 0.5753 (m-10) cc_final: 0.5550 (m-10) REVERT: D 339 TYR cc_start: 0.7006 (t80) cc_final: 0.6739 (t80) REVERT: D 342 CYS cc_start: 0.8214 (t) cc_final: 0.7939 (t) REVERT: D 345 MET cc_start: 0.6496 (ttm) cc_final: 0.6132 (ttt) REVERT: D 372 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7721 (pp) REVERT: D 434 PHE cc_start: 0.7771 (m-80) cc_final: 0.7142 (t80) REVERT: D 440 MET cc_start: 0.8227 (tmm) cc_final: 0.7585 (tpp) REVERT: D 483 GLN cc_start: 0.6901 (tt0) cc_final: 0.6466 (mp10) REVERT: D 528 MET cc_start: 0.7633 (tmm) cc_final: 0.7294 (tmm) REVERT: D 542 ASP cc_start: 0.6466 (t70) cc_final: 0.5696 (t0) REVERT: D 583 TRP cc_start: 0.7468 (t60) cc_final: 0.7045 (t60) REVERT: D 591 GLU cc_start: 0.8255 (tt0) cc_final: 0.7926 (tm-30) REVERT: D 594 ARG cc_start: 0.7465 (ttm110) cc_final: 0.7093 (mtp-110) REVERT: D 613 TRP cc_start: 0.8113 (t-100) cc_final: 0.7770 (t-100) REVERT: D 629 TRP cc_start: 0.6198 (m-10) cc_final: 0.5942 (m-10) outliers start: 103 outliers final: 45 residues processed: 621 average time/residue: 0.2729 time to fit residues: 268.4581 Evaluate side-chains 564 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 511 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 204 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 306 GLN A 464 ASN B 31 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 ASN C 546 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19484 Z= 0.225 Angle : 0.746 13.755 26440 Z= 0.358 Chirality : 0.043 0.242 3012 Planarity : 0.004 0.036 3336 Dihedral : 5.289 46.839 2598 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 4.84 % Allowed : 21.22 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2356 helix: 0.74 (0.14), residues: 1384 sheet: -3.35 (0.47), residues: 56 loop : -2.40 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 629 HIS 0.005 0.001 HIS D 522 PHE 0.025 0.002 PHE B 531 TYR 0.020 0.002 TYR B 467 ARG 0.005 0.000 ARG C 492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 544 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: A 118 GLN cc_start: 0.7144 (tt0) cc_final: 0.6922 (tt0) REVERT: A 164 GLU cc_start: 0.6737 (pm20) cc_final: 0.5813 (pt0) REVERT: A 184 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8647 (mt-10) REVERT: A 185 HIS cc_start: 0.7145 (m90) cc_final: 0.6882 (m90) REVERT: A 228 HIS cc_start: 0.6296 (m-70) cc_final: 0.5093 (p-80) REVERT: A 301 LYS cc_start: 0.7713 (mtpp) cc_final: 0.6983 (mtmt) REVERT: A 311 THR cc_start: 0.6375 (OUTLIER) cc_final: 0.5889 (p) REVERT: A 315 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7657 (mp0) REVERT: A 342 CYS cc_start: 0.8138 (t) cc_final: 0.7931 (t) REVERT: A 345 MET cc_start: 0.6236 (ttm) cc_final: 0.5974 (ttp) REVERT: A 434 PHE cc_start: 0.7761 (m-80) cc_final: 0.7208 (t80) REVERT: A 487 PHE cc_start: 0.7444 (m-80) cc_final: 0.7202 (m-80) REVERT: A 528 MET cc_start: 0.7633 (tmm) cc_final: 0.7163 (tmm) REVERT: A 538 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6450 (mp) REVERT: A 542 ASP cc_start: 0.6420 (t0) cc_final: 0.6178 (t0) REVERT: A 546 ASN cc_start: 0.7987 (t0) cc_final: 0.7684 (t0) REVERT: A 577 MET cc_start: 0.7117 (mtm) cc_final: 0.6847 (mtp) REVERT: A 583 TRP cc_start: 0.7307 (t60) cc_final: 0.6909 (t60) REVERT: A 591 GLU cc_start: 0.8212 (tt0) cc_final: 0.7540 (tm-30) REVERT: A 594 ARG cc_start: 0.7455 (ttm110) cc_final: 0.7116 (mtp-110) REVERT: B 45 TRP cc_start: 0.7344 (t-100) cc_final: 0.6990 (m100) REVERT: B 118 GLN cc_start: 0.6361 (tm-30) cc_final: 0.5780 (tm-30) REVERT: B 130 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7072 (mmm) REVERT: B 185 HIS cc_start: 0.7059 (m90) cc_final: 0.6810 (m90) REVERT: B 218 LEU cc_start: 0.8480 (tp) cc_final: 0.8232 (tp) REVERT: B 228 HIS cc_start: 0.6290 (m-70) cc_final: 0.5182 (p-80) REVERT: B 281 THR cc_start: 0.7955 (m) cc_final: 0.7656 (p) REVERT: B 284 ASP cc_start: 0.8196 (t0) cc_final: 0.7986 (t0) REVERT: B 294 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7582 (mt-10) REVERT: B 297 ILE cc_start: 0.6634 (OUTLIER) cc_final: 0.6425 (tp) REVERT: B 315 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7674 (mp0) REVERT: B 339 TYR cc_start: 0.7039 (t80) cc_final: 0.6604 (t80) REVERT: B 342 CYS cc_start: 0.8130 (t) cc_final: 0.7884 (t) REVERT: B 345 MET cc_start: 0.7715 (mmp) cc_final: 0.6373 (ttt) REVERT: B 373 LEU cc_start: 0.7685 (mp) cc_final: 0.6547 (tt) REVERT: B 390 LEU cc_start: 0.8805 (mt) cc_final: 0.8546 (tp) REVERT: B 434 PHE cc_start: 0.7682 (m-80) cc_final: 0.7121 (t80) REVERT: B 440 MET cc_start: 0.7927 (tmm) cc_final: 0.7464 (tpp) REVERT: B 487 PHE cc_start: 0.7777 (m-80) cc_final: 0.7567 (m-10) REVERT: B 491 MET cc_start: 0.6927 (mmm) cc_final: 0.6475 (ttp) REVERT: B 546 ASN cc_start: 0.8373 (t0) cc_final: 0.7750 (t0) REVERT: B 567 THR cc_start: 0.7105 (m) cc_final: 0.6900 (m) REVERT: B 583 TRP cc_start: 0.7148 (t60) cc_final: 0.6829 (t60) REVERT: B 618 ILE cc_start: 0.7290 (mm) cc_final: 0.6722 (tp) REVERT: C 130 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7009 (tpt) REVERT: C 184 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8648 (mt-10) REVERT: C 228 HIS cc_start: 0.6439 (m-70) cc_final: 0.5159 (p-80) REVERT: C 250 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7695 (tm-30) REVERT: C 277 LEU cc_start: 0.6985 (tp) cc_final: 0.6767 (mt) REVERT: C 282 GLU cc_start: 0.7907 (mp0) cc_final: 0.7680 (mp0) REVERT: C 315 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7688 (mp0) REVERT: C 339 TYR cc_start: 0.6915 (t80) cc_final: 0.6629 (t80) REVERT: C 345 MET cc_start: 0.7922 (mmm) cc_final: 0.6966 (ttt) REVERT: C 434 PHE cc_start: 0.7962 (m-80) cc_final: 0.7353 (t80) REVERT: C 440 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7703 (tmm) REVERT: C 528 MET cc_start: 0.7532 (tmm) cc_final: 0.6929 (tmm) REVERT: C 542 ASP cc_start: 0.6535 (m-30) cc_final: 0.6122 (m-30) REVERT: C 546 ASN cc_start: 0.8164 (t0) cc_final: 0.7480 (t0) REVERT: C 583 TRP cc_start: 0.7137 (t60) cc_final: 0.6780 (t60) REVERT: C 591 GLU cc_start: 0.8140 (tt0) cc_final: 0.7477 (tm-30) REVERT: C 594 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7114 (mtp-110) REVERT: C 616 SER cc_start: 0.8480 (t) cc_final: 0.7776 (p) REVERT: C 629 TRP cc_start: 0.7254 (m-10) cc_final: 0.6944 (m-10) REVERT: D 218 LEU cc_start: 0.8641 (tp) cc_final: 0.8363 (tp) REVERT: D 222 TYR cc_start: 0.8352 (m-80) cc_final: 0.8007 (m-10) REVERT: D 228 HIS cc_start: 0.6488 (m-70) cc_final: 0.5169 (p-80) REVERT: D 282 GLU cc_start: 0.7565 (mp0) cc_final: 0.6977 (mp0) REVERT: D 315 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: D 339 TYR cc_start: 0.7032 (t80) cc_final: 0.6704 (t80) REVERT: D 345 MET cc_start: 0.6434 (ttm) cc_final: 0.6169 (ttt) REVERT: D 434 PHE cc_start: 0.7839 (m-80) cc_final: 0.7210 (t80) REVERT: D 440 MET cc_start: 0.8210 (tmm) cc_final: 0.7510 (tpp) REVERT: D 483 GLN cc_start: 0.6861 (tt0) cc_final: 0.6537 (mp10) REVERT: D 542 ASP cc_start: 0.5884 (t70) cc_final: 0.5541 (t0) REVERT: D 546 ASN cc_start: 0.7594 (t0) cc_final: 0.7153 (t0) REVERT: D 583 TRP cc_start: 0.7378 (t60) cc_final: 0.6866 (t60) REVERT: D 591 GLU cc_start: 0.8232 (tt0) cc_final: 0.7723 (tm-30) REVERT: D 594 ARG cc_start: 0.7380 (ttm110) cc_final: 0.6936 (mtp-110) outliers start: 100 outliers final: 42 residues processed: 595 average time/residue: 0.2561 time to fit residues: 241.4706 Evaluate side-chains 549 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 499 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 8.9990 chunk 129 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 57 optimal weight: 0.2980 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19484 Z= 0.206 Angle : 0.755 14.239 26440 Z= 0.355 Chirality : 0.044 0.272 3012 Planarity : 0.004 0.036 3336 Dihedral : 5.183 47.579 2598 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.07 % Allowed : 23.69 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2356 helix: 0.91 (0.14), residues: 1372 sheet: -2.81 (0.56), residues: 56 loop : -2.28 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 613 HIS 0.004 0.001 HIS A 185 PHE 0.023 0.002 PHE C 256 TYR 0.015 0.001 TYR B 270 ARG 0.006 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 516 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: A 130 MET cc_start: 0.7262 (mmt) cc_final: 0.6949 (tpt) REVERT: A 164 GLU cc_start: 0.6682 (pm20) cc_final: 0.5761 (pt0) REVERT: A 222 TYR cc_start: 0.8236 (m-80) cc_final: 0.7911 (m-80) REVERT: A 228 HIS cc_start: 0.6301 (m-70) cc_final: 0.5095 (p-80) REVERT: A 311 THR cc_start: 0.6214 (OUTLIER) cc_final: 0.5582 (p) REVERT: A 315 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7664 (mp0) REVERT: A 345 MET cc_start: 0.6215 (ttm) cc_final: 0.5966 (ttp) REVERT: A 434 PHE cc_start: 0.7772 (m-80) cc_final: 0.7322 (t80) REVERT: A 440 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6873 (tpp) REVERT: A 442 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8012 (mtp) REVERT: A 454 MET cc_start: 0.6731 (ttm) cc_final: 0.6483 (ttm) REVERT: A 487 PHE cc_start: 0.7411 (m-80) cc_final: 0.7165 (m-80) REVERT: A 528 MET cc_start: 0.7625 (tmm) cc_final: 0.7316 (tmm) REVERT: A 538 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6575 (mp) REVERT: A 546 ASN cc_start: 0.8047 (t0) cc_final: 0.7577 (t0) REVERT: A 583 TRP cc_start: 0.7287 (t60) cc_final: 0.6925 (t60) REVERT: A 591 GLU cc_start: 0.8224 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 594 ARG cc_start: 0.7463 (ttm110) cc_final: 0.7119 (mtp180) REVERT: B 96 MET cc_start: 0.8487 (tmm) cc_final: 0.8034 (mtm) REVERT: B 110 MET cc_start: 0.7100 (mmm) cc_final: 0.6894 (mmm) REVERT: B 118 GLN cc_start: 0.6362 (tm-30) cc_final: 0.5799 (tm-30) REVERT: B 228 HIS cc_start: 0.6390 (m-70) cc_final: 0.5187 (p-80) REVERT: B 281 THR cc_start: 0.8106 (m) cc_final: 0.7643 (p) REVERT: B 282 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 294 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7393 (mm-30) REVERT: B 297 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6213 (tp) REVERT: B 301 LYS cc_start: 0.7815 (mtpp) cc_final: 0.7437 (mtmt) REVERT: B 315 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7641 (mp0) REVERT: B 342 CYS cc_start: 0.8177 (t) cc_final: 0.7932 (t) REVERT: B 345 MET cc_start: 0.7782 (mmp) cc_final: 0.6577 (ttt) REVERT: B 373 LEU cc_start: 0.7746 (mp) cc_final: 0.6502 (tt) REVERT: B 390 LEU cc_start: 0.8814 (mt) cc_final: 0.8567 (tp) REVERT: B 434 PHE cc_start: 0.7850 (m-80) cc_final: 0.7273 (t80) REVERT: B 440 MET cc_start: 0.7965 (tmm) cc_final: 0.7504 (tpp) REVERT: B 491 MET cc_start: 0.6946 (mmm) cc_final: 0.6457 (ttp) REVERT: B 546 ASN cc_start: 0.8201 (t0) cc_final: 0.7837 (t0) REVERT: B 567 THR cc_start: 0.7123 (m) cc_final: 0.6908 (m) REVERT: B 583 TRP cc_start: 0.7154 (t60) cc_final: 0.6841 (t60) REVERT: C 130 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6969 (tpt) REVERT: C 216 TYR cc_start: 0.7904 (t80) cc_final: 0.7672 (t80) REVERT: C 222 TYR cc_start: 0.8210 (m-80) cc_final: 0.7880 (m-80) REVERT: C 228 HIS cc_start: 0.6493 (m-70) cc_final: 0.5205 (p-80) REVERT: C 279 ASP cc_start: 0.6976 (m-30) cc_final: 0.6690 (p0) REVERT: C 282 GLU cc_start: 0.7987 (mp0) cc_final: 0.7523 (mp0) REVERT: C 315 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7720 (mp0) REVERT: C 339 TYR cc_start: 0.6901 (t80) cc_final: 0.6593 (t80) REVERT: C 345 MET cc_start: 0.7826 (mmm) cc_final: 0.6929 (ttt) REVERT: C 434 PHE cc_start: 0.8008 (m-80) cc_final: 0.7374 (t80) REVERT: C 440 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: C 515 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8577 (tp30) REVERT: C 528 MET cc_start: 0.7606 (tmm) cc_final: 0.6947 (tmm) REVERT: C 546 ASN cc_start: 0.8191 (t0) cc_final: 0.7549 (t0) REVERT: C 583 TRP cc_start: 0.7080 (t60) cc_final: 0.6726 (t60) REVERT: C 591 GLU cc_start: 0.8155 (tt0) cc_final: 0.7591 (tm-30) REVERT: C 594 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7161 (mtp-110) REVERT: C 616 SER cc_start: 0.8521 (t) cc_final: 0.8013 (p) REVERT: D 118 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7264 (tp40) REVERT: D 222 TYR cc_start: 0.8430 (m-80) cc_final: 0.7910 (m-80) REVERT: D 228 HIS cc_start: 0.6472 (m-70) cc_final: 0.5154 (p-80) REVERT: D 261 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7678 (tm-30) REVERT: D 294 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8007 (mm-30) REVERT: D 315 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: D 339 TYR cc_start: 0.7042 (t80) cc_final: 0.6753 (t80) REVERT: D 434 PHE cc_start: 0.7946 (m-80) cc_final: 0.7315 (t80) REVERT: D 440 MET cc_start: 0.8276 (tmm) cc_final: 0.7467 (tpp) REVERT: D 483 GLN cc_start: 0.6746 (tt0) cc_final: 0.6376 (mp10) REVERT: D 538 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6457 (mp) REVERT: D 542 ASP cc_start: 0.5655 (t70) cc_final: 0.5382 (t0) REVERT: D 546 ASN cc_start: 0.7676 (t0) cc_final: 0.7294 (t0) REVERT: D 583 TRP cc_start: 0.7314 (t60) cc_final: 0.6863 (t60) REVERT: D 591 GLU cc_start: 0.8269 (tt0) cc_final: 0.7768 (tm-30) REVERT: D 594 ARG cc_start: 0.7426 (ttm110) cc_final: 0.6965 (mtp-110) outliers start: 84 outliers final: 40 residues processed: 555 average time/residue: 0.2928 time to fit residues: 261.2788 Evaluate side-chains 535 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 485 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 chunk 189 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19484 Z= 0.182 Angle : 0.754 15.128 26440 Z= 0.349 Chirality : 0.043 0.268 3012 Planarity : 0.004 0.032 3336 Dihedral : 5.062 47.384 2598 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.25 % Favored : 90.70 % Rotamer: Outliers : 3.78 % Allowed : 24.66 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2356 helix: 1.08 (0.14), residues: 1380 sheet: -2.48 (0.50), residues: 56 loop : -2.20 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 629 HIS 0.005 0.001 HIS A 185 PHE 0.017 0.001 PHE B 531 TYR 0.013 0.001 TYR B 270 ARG 0.008 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 501 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: A 130 MET cc_start: 0.7193 (mmt) cc_final: 0.6307 (tpt) REVERT: A 164 GLU cc_start: 0.6554 (pm20) cc_final: 0.5418 (pt0) REVERT: A 222 TYR cc_start: 0.8176 (m-80) cc_final: 0.7910 (m-80) REVERT: A 228 HIS cc_start: 0.6316 (m-70) cc_final: 0.5098 (p-80) REVERT: A 311 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.5254 (p) REVERT: A 315 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7629 (mp0) REVERT: A 339 TYR cc_start: 0.7136 (t80) cc_final: 0.6782 (t80) REVERT: A 345 MET cc_start: 0.6174 (ttm) cc_final: 0.5928 (ttp) REVERT: A 434 PHE cc_start: 0.7833 (m-80) cc_final: 0.7313 (t80) REVERT: A 440 MET cc_start: 0.7853 (ppp) cc_final: 0.7167 (tpp) REVERT: A 442 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8080 (mtp) REVERT: A 454 MET cc_start: 0.6731 (ttm) cc_final: 0.6507 (ttm) REVERT: A 487 PHE cc_start: 0.7346 (m-80) cc_final: 0.7089 (m-80) REVERT: A 489 ASP cc_start: 0.5448 (t70) cc_final: 0.4898 (t70) REVERT: A 492 ARG cc_start: 0.6371 (ptt90) cc_final: 0.6151 (ptm160) REVERT: A 526 TYR cc_start: 0.7404 (t80) cc_final: 0.7177 (t80) REVERT: A 528 MET cc_start: 0.7531 (tmm) cc_final: 0.7163 (tmm) REVERT: A 538 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6436 (mp) REVERT: A 546 ASN cc_start: 0.8057 (t0) cc_final: 0.7592 (t0) REVERT: A 583 TRP cc_start: 0.7261 (t60) cc_final: 0.6911 (t60) REVERT: A 591 GLU cc_start: 0.8235 (tt0) cc_final: 0.7635 (tm-30) REVERT: A 594 ARG cc_start: 0.7435 (ttm110) cc_final: 0.7204 (mtm-85) REVERT: B 118 GLN cc_start: 0.6704 (tm-30) cc_final: 0.6023 (tm-30) REVERT: B 228 HIS cc_start: 0.6379 (m-70) cc_final: 0.5215 (p-80) REVERT: B 281 THR cc_start: 0.8105 (m) cc_final: 0.7583 (p) REVERT: B 282 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 294 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7383 (mm-30) REVERT: B 297 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6167 (tp) REVERT: B 301 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7402 (mtmt) REVERT: B 315 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7644 (mp0) REVERT: B 339 TYR cc_start: 0.7200 (t80) cc_final: 0.6782 (t80) REVERT: B 342 CYS cc_start: 0.8124 (t) cc_final: 0.7909 (t) REVERT: B 345 MET cc_start: 0.7732 (mmp) cc_final: 0.6543 (ttt) REVERT: B 373 LEU cc_start: 0.7794 (mp) cc_final: 0.6503 (tt) REVERT: B 390 LEU cc_start: 0.8841 (mt) cc_final: 0.8626 (tp) REVERT: B 434 PHE cc_start: 0.7859 (m-80) cc_final: 0.7295 (t80) REVERT: B 440 MET cc_start: 0.7970 (tmm) cc_final: 0.7489 (tpp) REVERT: B 491 MET cc_start: 0.6990 (mmm) cc_final: 0.6536 (ttp) REVERT: B 546 ASN cc_start: 0.8166 (t0) cc_final: 0.7657 (t0) REVERT: B 567 THR cc_start: 0.7092 (m) cc_final: 0.6873 (m) REVERT: B 583 TRP cc_start: 0.7161 (t60) cc_final: 0.6847 (t60) REVERT: B 591 GLU cc_start: 0.8099 (tt0) cc_final: 0.7516 (tm-30) REVERT: C 34 ASP cc_start: 0.8189 (m-30) cc_final: 0.7979 (m-30) REVERT: C 130 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6457 (tpt) REVERT: C 222 TYR cc_start: 0.8334 (m-80) cc_final: 0.7861 (m-80) REVERT: C 228 HIS cc_start: 0.6404 (m-70) cc_final: 0.5147 (p-80) REVERT: C 261 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7722 (tm-30) REVERT: C 282 GLU cc_start: 0.7938 (mp0) cc_final: 0.7729 (mp0) REVERT: C 315 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7757 (mp0) REVERT: C 339 TYR cc_start: 0.6921 (t80) cc_final: 0.6585 (t80) REVERT: C 345 MET cc_start: 0.7794 (mmm) cc_final: 0.6966 (ttt) REVERT: C 434 PHE cc_start: 0.8061 (m-80) cc_final: 0.7403 (t80) REVERT: C 440 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7700 (tmm) REVERT: C 528 MET cc_start: 0.7610 (tmm) cc_final: 0.6883 (tmm) REVERT: C 546 ASN cc_start: 0.8213 (t0) cc_final: 0.7591 (t0) REVERT: C 591 GLU cc_start: 0.8236 (tt0) cc_final: 0.7589 (tm-30) REVERT: C 594 ARG cc_start: 0.7490 (ttm110) cc_final: 0.7076 (mtp-110) REVERT: C 616 SER cc_start: 0.8480 (t) cc_final: 0.7768 (p) REVERT: D 222 TYR cc_start: 0.8446 (m-80) cc_final: 0.7889 (m-80) REVERT: D 228 HIS cc_start: 0.6515 (m-70) cc_final: 0.5258 (p-80) REVERT: D 261 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7728 (tm-30) REVERT: D 294 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7989 (mm-30) REVERT: D 315 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: D 339 TYR cc_start: 0.7041 (t80) cc_final: 0.6738 (t80) REVERT: D 434 PHE cc_start: 0.7968 (m-80) cc_final: 0.7332 (t80) REVERT: D 440 MET cc_start: 0.8215 (tmm) cc_final: 0.7563 (tpp) REVERT: D 538 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6548 (mp) REVERT: D 546 ASN cc_start: 0.7718 (t0) cc_final: 0.7125 (t0) REVERT: D 583 TRP cc_start: 0.7331 (t60) cc_final: 0.6983 (t60) REVERT: D 591 GLU cc_start: 0.8276 (tt0) cc_final: 0.7737 (tm-30) REVERT: D 594 ARG cc_start: 0.7405 (ttm110) cc_final: 0.6934 (mtp-110) outliers start: 78 outliers final: 43 residues processed: 536 average time/residue: 0.2809 time to fit residues: 236.9822 Evaluate side-chains 526 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 474 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 472 PHE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 600 THR 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: 2.9990 chunk 130 optimal weight: 0.0870 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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 118 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 267 GLN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 257 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19484 Z= 0.204 Angle : 0.759 15.789 26440 Z= 0.354 Chirality : 0.044 0.242 3012 Planarity : 0.004 0.039 3336 Dihedral : 4.992 48.137 2598 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.97 % Allowed : 24.76 % Favored : 71.27 % 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: -0.40 (0.18), residues: 2356 helix: 1.05 (0.14), residues: 1396 sheet: -2.49 (0.49), residues: 56 loop : -2.28 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 629 HIS 0.004 0.001 HIS A 185 PHE 0.018 0.001 PHE A 553 TYR 0.014 0.001 TYR D 526 ARG 0.007 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 505 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6828 (mmt) cc_final: 0.6045 (mmm) REVERT: A 164 GLU cc_start: 0.6685 (pm20) cc_final: 0.5646 (pt0) REVERT: A 222 TYR cc_start: 0.8313 (m-80) cc_final: 0.7961 (m-80) REVERT: A 228 HIS cc_start: 0.6310 (m-70) cc_final: 0.5087 (p-80) REVERT: A 311 THR cc_start: 0.6014 (OUTLIER) cc_final: 0.5445 (p) REVERT: A 315 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7696 (mp0) REVERT: A 345 MET cc_start: 0.6322 (ttm) cc_final: 0.6056 (ttp) REVERT: A 390 LEU cc_start: 0.8761 (mt) cc_final: 0.8539 (tp) REVERT: A 434 PHE cc_start: 0.7851 (m-80) cc_final: 0.7296 (t80) REVERT: A 440 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7096 (mmm) REVERT: A 442 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8116 (mtp) REVERT: A 454 MET cc_start: 0.6782 (ttm) cc_final: 0.6555 (ttm) REVERT: A 487 PHE cc_start: 0.7260 (m-80) cc_final: 0.6990 (m-80) REVERT: A 489 ASP cc_start: 0.5425 (t70) cc_final: 0.5076 (t70) REVERT: A 515 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7336 (mm-30) REVERT: A 526 TYR cc_start: 0.7469 (t80) cc_final: 0.7237 (t80) REVERT: A 528 MET cc_start: 0.7526 (tmm) cc_final: 0.7314 (tpp) REVERT: A 538 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6535 (mp) REVERT: A 542 ASP cc_start: 0.5836 (m-30) cc_final: 0.4525 (m-30) REVERT: A 546 ASN cc_start: 0.8069 (t0) cc_final: 0.7586 (t0) REVERT: A 583 TRP cc_start: 0.7293 (t60) cc_final: 0.6908 (t60) REVERT: A 591 GLU cc_start: 0.8288 (tt0) cc_final: 0.7746 (tm-30) REVERT: A 594 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7220 (mtm-85) REVERT: B 96 MET cc_start: 0.8363 (tmm) cc_final: 0.7878 (mtm) REVERT: B 228 HIS cc_start: 0.6324 (m-70) cc_final: 0.5118 (p-80) REVERT: B 261 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7623 (tm-30) REVERT: B 282 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: B 289 GLU cc_start: 0.7070 (tt0) cc_final: 0.6779 (tt0) REVERT: B 294 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7588 (mt-10) REVERT: B 297 ILE cc_start: 0.6367 (OUTLIER) cc_final: 0.6159 (tp) REVERT: B 301 LYS cc_start: 0.7807 (mtpp) cc_final: 0.7391 (mtmt) REVERT: B 315 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7664 (mp0) REVERT: B 339 TYR cc_start: 0.7151 (t80) cc_final: 0.6698 (t80) REVERT: B 342 CYS cc_start: 0.8129 (t) cc_final: 0.7918 (t) REVERT: B 345 MET cc_start: 0.7789 (mmp) cc_final: 0.6598 (ttt) REVERT: B 373 LEU cc_start: 0.7639 (mp) cc_final: 0.6351 (tt) REVERT: B 390 LEU cc_start: 0.8851 (mt) cc_final: 0.8635 (tp) REVERT: B 434 PHE cc_start: 0.7993 (m-80) cc_final: 0.7403 (t80) REVERT: B 440 MET cc_start: 0.7872 (tmm) cc_final: 0.7496 (tpp) REVERT: B 491 MET cc_start: 0.7069 (mmm) cc_final: 0.6646 (ttp) REVERT: B 546 ASN cc_start: 0.8142 (t0) cc_final: 0.7648 (t0) REVERT: B 567 THR cc_start: 0.7064 (m) cc_final: 0.6831 (m) REVERT: B 583 TRP cc_start: 0.7201 (t60) cc_final: 0.6861 (t60) REVERT: B 591 GLU cc_start: 0.8104 (tt0) cc_final: 0.7442 (tm-30) REVERT: C 34 ASP cc_start: 0.8163 (m-30) cc_final: 0.7940 (m-30) REVERT: C 130 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6810 (mmm) REVERT: C 174 ASN cc_start: 0.7898 (m110) cc_final: 0.7635 (t0) REVERT: C 222 TYR cc_start: 0.8396 (m-80) cc_final: 0.7912 (m-80) REVERT: C 228 HIS cc_start: 0.6426 (m-70) cc_final: 0.5232 (p-80) REVERT: C 261 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7862 (tm-30) REVERT: C 301 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7229 (mmtt) REVERT: C 315 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7762 (mp0) REVERT: C 339 TYR cc_start: 0.6913 (t80) cc_final: 0.6626 (t80) REVERT: C 345 MET cc_start: 0.7678 (mmm) cc_final: 0.6847 (ttp) REVERT: C 346 CYS cc_start: 0.7905 (p) cc_final: 0.7202 (m) REVERT: C 434 PHE cc_start: 0.8109 (m-80) cc_final: 0.7437 (t80) REVERT: C 515 GLU cc_start: 0.8676 (tp30) cc_final: 0.8233 (mm-30) REVERT: C 528 MET cc_start: 0.7667 (tmm) cc_final: 0.6927 (tmm) REVERT: C 546 ASN cc_start: 0.8224 (t0) cc_final: 0.7630 (t0) REVERT: C 591 GLU cc_start: 0.8299 (tt0) cc_final: 0.7655 (tm-30) REVERT: C 594 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7085 (mtp-110) REVERT: C 616 SER cc_start: 0.8552 (t) cc_final: 0.7817 (p) REVERT: D 215 MET cc_start: 0.8863 (tpp) cc_final: 0.8518 (mpp) REVERT: D 222 TYR cc_start: 0.8473 (m-80) cc_final: 0.7866 (m-80) REVERT: D 228 HIS cc_start: 0.6525 (m-70) cc_final: 0.5305 (p-80) REVERT: D 261 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7759 (tm-30) REVERT: D 294 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8100 (mm-30) REVERT: D 315 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: D 339 TYR cc_start: 0.6994 (t80) cc_final: 0.6742 (t80) REVERT: D 434 PHE cc_start: 0.7909 (m-80) cc_final: 0.7277 (t80) REVERT: D 439 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7922 (m) REVERT: D 440 MET cc_start: 0.8191 (tmm) cc_final: 0.7574 (tpp) REVERT: D 442 MET cc_start: 0.8298 (mtm) cc_final: 0.8087 (mtp) REVERT: D 483 GLN cc_start: 0.6653 (tt0) cc_final: 0.6268 (mp10) REVERT: D 538 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6523 (mp) REVERT: D 546 ASN cc_start: 0.7789 (t0) cc_final: 0.7399 (t0) REVERT: D 583 TRP cc_start: 0.7391 (t60) cc_final: 0.6855 (t60) REVERT: D 591 GLU cc_start: 0.8243 (tt0) cc_final: 0.7718 (tm-30) REVERT: D 594 ARG cc_start: 0.7416 (ttm110) cc_final: 0.6925 (mtp-110) outliers start: 82 outliers final: 44 residues processed: 544 average time/residue: 0.2873 time to fit residues: 243.4750 Evaluate side-chains 532 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 478 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 600 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 44 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 118 GLN A 185 HIS ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 464 ASN B 596 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19484 Z= 0.193 Angle : 0.775 16.307 26440 Z= 0.357 Chirality : 0.044 0.338 3012 Planarity : 0.004 0.035 3336 Dihedral : 4.985 48.492 2598 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.13 % Favored : 90.83 % Rotamer: Outliers : 3.68 % Allowed : 25.68 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2356 helix: 1.01 (0.14), residues: 1404 sheet: -2.44 (0.49), residues: 56 loop : -2.32 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 629 HIS 0.004 0.001 HIS A 582 PHE 0.034 0.001 PHE B 553 TYR 0.017 0.001 TYR D 216 ARG 0.007 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 501 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: A 130 MET cc_start: 0.6927 (mmt) cc_final: 0.6068 (mmt) REVERT: A 164 GLU cc_start: 0.6684 (pm20) cc_final: 0.5622 (pt0) REVERT: A 213 CYS cc_start: 0.8384 (t) cc_final: 0.7978 (t) REVERT: A 222 TYR cc_start: 0.8303 (m-80) cc_final: 0.7958 (m-80) REVERT: A 228 HIS cc_start: 0.6283 (m-70) cc_final: 0.5079 (p-80) REVERT: A 301 LYS cc_start: 0.7129 (mtmt) cc_final: 0.6474 (mmtt) REVERT: A 311 THR cc_start: 0.6027 (OUTLIER) cc_final: 0.5448 (p) REVERT: A 315 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7718 (mp0) REVERT: A 339 TYR cc_start: 0.7074 (t80) cc_final: 0.6707 (t80) REVERT: A 345 MET cc_start: 0.6390 (ttm) cc_final: 0.6114 (ttp) REVERT: A 390 LEU cc_start: 0.8775 (mt) cc_final: 0.8562 (tp) REVERT: A 434 PHE cc_start: 0.7826 (m-80) cc_final: 0.7262 (t80) REVERT: A 440 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7170 (tpp) REVERT: A 442 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8168 (mtp) REVERT: A 454 MET cc_start: 0.6729 (ttm) cc_final: 0.6511 (ttm) REVERT: A 487 PHE cc_start: 0.7313 (m-80) cc_final: 0.7026 (m-80) REVERT: A 489 ASP cc_start: 0.5265 (t70) cc_final: 0.5063 (t70) REVERT: A 515 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7293 (mm-30) REVERT: A 526 TYR cc_start: 0.7455 (t80) cc_final: 0.7238 (t80) REVERT: A 538 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6569 (mp) REVERT: A 546 ASN cc_start: 0.8076 (t0) cc_final: 0.7539 (t0) REVERT: A 583 TRP cc_start: 0.7283 (t60) cc_final: 0.6916 (t60) REVERT: A 591 GLU cc_start: 0.8266 (tt0) cc_final: 0.7705 (tm-30) REVERT: A 594 ARG cc_start: 0.7424 (ttm110) cc_final: 0.7192 (mtm-85) REVERT: B 96 MET cc_start: 0.8331 (tmm) cc_final: 0.7867 (mtm) REVERT: B 118 GLN cc_start: 0.6579 (tm-30) cc_final: 0.6218 (tm-30) REVERT: B 209 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6350 (mttp) REVERT: B 228 HIS cc_start: 0.6394 (m-70) cc_final: 0.5264 (p-80) REVERT: B 261 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7634 (tm-30) REVERT: B 289 GLU cc_start: 0.7104 (tt0) cc_final: 0.6800 (tt0) REVERT: B 294 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7467 (mm-30) REVERT: B 301 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7400 (mtmt) REVERT: B 315 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7657 (mp0) REVERT: B 339 TYR cc_start: 0.7180 (t80) cc_final: 0.6756 (t80) REVERT: B 345 MET cc_start: 0.7776 (mmp) cc_final: 0.6591 (ttt) REVERT: B 373 LEU cc_start: 0.7614 (mp) cc_final: 0.6314 (tt) REVERT: B 390 LEU cc_start: 0.8871 (mt) cc_final: 0.8662 (tp) REVERT: B 434 PHE cc_start: 0.7907 (m-80) cc_final: 0.7322 (t80) REVERT: B 440 MET cc_start: 0.8127 (tmm) cc_final: 0.7604 (tpp) REVERT: B 491 MET cc_start: 0.7065 (mmm) cc_final: 0.6693 (ttp) REVERT: B 542 ASP cc_start: 0.6316 (m-30) cc_final: 0.5893 (m-30) REVERT: B 546 ASN cc_start: 0.8090 (t0) cc_final: 0.7773 (t0) REVERT: B 567 THR cc_start: 0.6958 (m) cc_final: 0.6722 (m) REVERT: B 583 TRP cc_start: 0.7209 (t60) cc_final: 0.6848 (t60) REVERT: B 591 GLU cc_start: 0.8148 (tt0) cc_final: 0.7652 (tm-30) REVERT: C 34 ASP cc_start: 0.8154 (m-30) cc_final: 0.7913 (m-30) REVERT: C 118 GLN cc_start: 0.6862 (tm-30) cc_final: 0.6430 (tm-30) REVERT: C 174 ASN cc_start: 0.7924 (m110) cc_final: 0.7607 (t0) REVERT: C 222 TYR cc_start: 0.8396 (m-80) cc_final: 0.7892 (m-80) REVERT: C 228 HIS cc_start: 0.6379 (m-70) cc_final: 0.5202 (p-80) REVERT: C 261 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7893 (tm-30) REVERT: C 301 LYS cc_start: 0.7703 (mtmt) cc_final: 0.7289 (mmtt) REVERT: C 315 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7774 (mp0) REVERT: C 339 TYR cc_start: 0.6957 (t80) cc_final: 0.6681 (t80) REVERT: C 345 MET cc_start: 0.7669 (mmm) cc_final: 0.6835 (ttp) REVERT: C 346 CYS cc_start: 0.7834 (p) cc_final: 0.7133 (m) REVERT: C 434 PHE cc_start: 0.8090 (m-80) cc_final: 0.7427 (t80) REVERT: C 439 THR cc_start: 0.7914 (t) cc_final: 0.7576 (m) REVERT: C 526 TYR cc_start: 0.7456 (t80) cc_final: 0.7253 (t80) REVERT: C 528 MET cc_start: 0.7603 (tmm) cc_final: 0.7055 (tmm) REVERT: C 546 ASN cc_start: 0.8240 (t0) cc_final: 0.7642 (t0) REVERT: C 591 GLU cc_start: 0.8200 (tt0) cc_final: 0.7591 (tm-30) REVERT: C 594 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7087 (mtp-110) REVERT: C 616 SER cc_start: 0.8646 (t) cc_final: 0.8041 (p) REVERT: D 222 TYR cc_start: 0.8447 (m-80) cc_final: 0.7821 (m-80) REVERT: D 228 HIS cc_start: 0.6457 (m-70) cc_final: 0.5269 (p-80) REVERT: D 261 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7674 (tm-30) REVERT: D 294 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8104 (mm-30) REVERT: D 315 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: D 339 TYR cc_start: 0.7057 (t80) cc_final: 0.6784 (t80) REVERT: D 434 PHE cc_start: 0.7967 (m-80) cc_final: 0.7338 (t80) REVERT: D 439 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7896 (m) REVERT: D 483 GLN cc_start: 0.6615 (tt0) cc_final: 0.6236 (mp10) REVERT: D 538 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6504 (mp) REVERT: D 546 ASN cc_start: 0.7818 (t0) cc_final: 0.7222 (t0) REVERT: D 583 TRP cc_start: 0.7305 (t60) cc_final: 0.6879 (t60) REVERT: D 591 GLU cc_start: 0.8297 (tt0) cc_final: 0.7819 (tm-30) REVERT: D 594 ARG cc_start: 0.7399 (ttm110) cc_final: 0.6919 (mtp-110) outliers start: 76 outliers final: 45 residues processed: 538 average time/residue: 0.2848 time to fit residues: 240.3580 Evaluate side-chains 533 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 479 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 4.9990 chunk 198 optimal weight: 0.3980 chunk 211 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 185 HIS A 257 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19484 Z= 0.214 Angle : 0.793 15.427 26440 Z= 0.368 Chirality : 0.045 0.347 3012 Planarity : 0.004 0.036 3336 Dihedral : 4.981 51.077 2598 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.15 % Allowed : 26.45 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2356 helix: 0.98 (0.14), residues: 1412 sheet: -2.37 (0.49), residues: 56 loop : -2.30 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 613 HIS 0.004 0.001 HIS B 582 PHE 0.035 0.001 PHE B 553 TYR 0.020 0.001 TYR C 467 ARG 0.007 0.000 ARG B 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 488 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: A 130 MET cc_start: 0.7031 (mmt) cc_final: 0.6132 (mmt) REVERT: A 164 GLU cc_start: 0.6767 (pm20) cc_final: 0.5808 (pt0) REVERT: A 213 CYS cc_start: 0.8407 (t) cc_final: 0.7957 (t) REVERT: A 222 TYR cc_start: 0.8346 (m-80) cc_final: 0.8009 (m-80) REVERT: A 228 HIS cc_start: 0.6323 (m-70) cc_final: 0.5131 (p-80) REVERT: A 255 MET cc_start: 0.7242 (mmm) cc_final: 0.6946 (mmm) REVERT: A 301 LYS cc_start: 0.7131 (mtmt) cc_final: 0.6497 (mmtt) REVERT: A 311 THR cc_start: 0.5900 (OUTLIER) cc_final: 0.5340 (p) REVERT: A 315 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7702 (mp0) REVERT: A 345 MET cc_start: 0.6451 (ttm) cc_final: 0.6173 (ttp) REVERT: A 434 PHE cc_start: 0.7836 (m-80) cc_final: 0.7261 (t80) REVERT: A 440 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7173 (tpp) REVERT: A 442 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8042 (mtp) REVERT: A 454 MET cc_start: 0.6714 (ttm) cc_final: 0.6503 (ttm) REVERT: A 487 PHE cc_start: 0.7414 (m-80) cc_final: 0.7137 (m-80) REVERT: A 489 ASP cc_start: 0.5219 (t70) cc_final: 0.4986 (t70) REVERT: A 515 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7279 (mm-30) REVERT: A 526 TYR cc_start: 0.7449 (t80) cc_final: 0.7221 (t80) REVERT: A 528 MET cc_start: 0.6873 (tpp) cc_final: 0.6612 (tpp) REVERT: A 538 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6596 (mp) REVERT: A 546 ASN cc_start: 0.8032 (t0) cc_final: 0.7526 (t0) REVERT: A 583 TRP cc_start: 0.7178 (t60) cc_final: 0.6868 (t60) REVERT: A 591 GLU cc_start: 0.8299 (tt0) cc_final: 0.7739 (tm-30) REVERT: A 594 ARG cc_start: 0.7439 (ttm110) cc_final: 0.7200 (mtm-85) REVERT: B 130 MET cc_start: 0.7055 (mmt) cc_final: 0.6316 (mmt) REVERT: B 209 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6271 (mttp) REVERT: B 213 CYS cc_start: 0.8494 (t) cc_final: 0.7954 (t) REVERT: B 228 HIS cc_start: 0.6425 (m-70) cc_final: 0.5221 (p-80) REVERT: B 261 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7562 (tm-30) REVERT: B 294 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7633 (mt-10) REVERT: B 301 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7409 (mtmt) REVERT: B 315 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7802 (mp0) REVERT: B 339 TYR cc_start: 0.6968 (t80) cc_final: 0.6627 (t80) REVERT: B 345 MET cc_start: 0.7842 (mmp) cc_final: 0.6578 (ttt) REVERT: B 373 LEU cc_start: 0.7663 (mp) cc_final: 0.6372 (tt) REVERT: B 390 LEU cc_start: 0.8877 (mt) cc_final: 0.8676 (tp) REVERT: B 434 PHE cc_start: 0.8012 (m-80) cc_final: 0.7413 (t80) REVERT: B 440 MET cc_start: 0.8175 (tmm) cc_final: 0.7650 (tpp) REVERT: B 491 MET cc_start: 0.7155 (mmm) cc_final: 0.6755 (ttp) REVERT: B 519 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6276 (mp0) REVERT: B 546 ASN cc_start: 0.8121 (t0) cc_final: 0.7728 (t0) REVERT: B 567 THR cc_start: 0.6943 (m) cc_final: 0.6698 (m) REVERT: B 583 TRP cc_start: 0.7201 (t60) cc_final: 0.6854 (t60) REVERT: B 591 GLU cc_start: 0.8130 (tt0) cc_final: 0.7695 (tm-30) REVERT: B 632 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8384 (ptt90) REVERT: C 174 ASN cc_start: 0.7973 (m110) cc_final: 0.7636 (t0) REVERT: C 222 TYR cc_start: 0.8426 (m-80) cc_final: 0.7864 (m-80) REVERT: C 228 HIS cc_start: 0.6223 (m-70) cc_final: 0.5064 (p-80) REVERT: C 261 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7887 (tm-30) REVERT: C 301 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7322 (mmtt) REVERT: C 315 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7805 (mp0) REVERT: C 339 TYR cc_start: 0.6958 (t80) cc_final: 0.6699 (t80) REVERT: C 345 MET cc_start: 0.7691 (mmm) cc_final: 0.6886 (ttp) REVERT: C 434 PHE cc_start: 0.8113 (m-80) cc_final: 0.7452 (t80) REVERT: C 439 THR cc_start: 0.7905 (t) cc_final: 0.7567 (m) REVERT: C 526 TYR cc_start: 0.7474 (t80) cc_final: 0.7253 (t80) REVERT: C 528 MET cc_start: 0.7593 (tmm) cc_final: 0.7027 (tmm) REVERT: C 546 ASN cc_start: 0.8239 (t0) cc_final: 0.7640 (t0) REVERT: C 591 GLU cc_start: 0.8212 (tt0) cc_final: 0.7639 (tm-30) REVERT: C 594 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7093 (mtp-110) REVERT: C 616 SER cc_start: 0.8577 (t) cc_final: 0.7932 (p) REVERT: D 130 MET cc_start: 0.7405 (tpt) cc_final: 0.7007 (mmt) REVERT: D 173 VAL cc_start: 0.7912 (m) cc_final: 0.7619 (m) REVERT: D 213 CYS cc_start: 0.8633 (t) cc_final: 0.8229 (t) REVERT: D 215 MET cc_start: 0.8735 (tpp) cc_final: 0.8497 (mtt) REVERT: D 222 TYR cc_start: 0.8386 (m-80) cc_final: 0.7619 (m-80) REVERT: D 228 HIS cc_start: 0.6472 (m-70) cc_final: 0.5262 (p-80) REVERT: D 261 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7728 (tm-30) REVERT: D 315 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: D 339 TYR cc_start: 0.7052 (t80) cc_final: 0.6832 (t80) REVERT: D 434 PHE cc_start: 0.8049 (m-80) cc_final: 0.7420 (t80) REVERT: D 439 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7849 (m) REVERT: D 483 GLN cc_start: 0.6669 (tt0) cc_final: 0.6287 (mp10) REVERT: D 528 MET cc_start: 0.7137 (tpp) cc_final: 0.6817 (tpp) REVERT: D 538 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6526 (mp) REVERT: D 546 ASN cc_start: 0.7925 (t0) cc_final: 0.7489 (t0) REVERT: D 583 TRP cc_start: 0.7306 (t60) cc_final: 0.6863 (t60) REVERT: D 591 GLU cc_start: 0.8284 (tt0) cc_final: 0.7811 (tm-30) REVERT: D 594 ARG cc_start: 0.7407 (ttm110) cc_final: 0.6926 (mtp-110) outliers start: 65 outliers final: 46 residues processed: 521 average time/residue: 0.2783 time to fit residues: 229.2758 Evaluate side-chains 528 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 473 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 118 GLN A 185 HIS A 257 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 185 HIS D 197 ASN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.7668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 19484 Z= 0.242 Angle : 0.821 15.332 26440 Z= 0.381 Chirality : 0.046 0.309 3012 Planarity : 0.004 0.036 3336 Dihedral : 5.004 51.397 2598 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.76 % Allowed : 26.94 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2356 helix: 1.04 (0.14), residues: 1392 sheet: -2.24 (0.51), residues: 56 loop : -2.19 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 613 HIS 0.006 0.001 HIS D 522 PHE 0.038 0.002 PHE A 553 TYR 0.044 0.002 TYR D 526 ARG 0.007 0.000 ARG B 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 492 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLN cc_start: 0.7361 (tt0) cc_final: 0.6873 (tt0) REVERT: A 130 MET cc_start: 0.7002 (mmt) cc_final: 0.6097 (mmt) REVERT: A 164 GLU cc_start: 0.6854 (pm20) cc_final: 0.5916 (pt0) REVERT: A 213 CYS cc_start: 0.8322 (t) cc_final: 0.7898 (t) REVERT: A 222 TYR cc_start: 0.8308 (m-80) cc_final: 0.7911 (m-80) REVERT: A 228 HIS cc_start: 0.6350 (m-70) cc_final: 0.5286 (p-80) REVERT: A 301 LYS cc_start: 0.7229 (mtmt) cc_final: 0.6637 (mmtt) REVERT: A 311 THR cc_start: 0.5945 (OUTLIER) cc_final: 0.5385 (p) REVERT: A 315 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7724 (mp0) REVERT: A 339 TYR cc_start: 0.7024 (t80) cc_final: 0.6715 (t80) REVERT: A 345 MET cc_start: 0.6470 (ttm) cc_final: 0.6169 (ttp) REVERT: A 434 PHE cc_start: 0.7852 (m-80) cc_final: 0.7252 (t80) REVERT: A 440 MET cc_start: 0.7883 (ppp) cc_final: 0.7138 (mmm) REVERT: A 442 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7993 (mtp) REVERT: A 454 MET cc_start: 0.6725 (ttm) cc_final: 0.6521 (ttm) REVERT: A 487 PHE cc_start: 0.7417 (m-80) cc_final: 0.7200 (m-80) REVERT: A 515 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7293 (mm-30) REVERT: A 538 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6618 (mp) REVERT: A 546 ASN cc_start: 0.8109 (t0) cc_final: 0.7764 (t0) REVERT: A 583 TRP cc_start: 0.7211 (t60) cc_final: 0.6868 (t60) REVERT: A 591 GLU cc_start: 0.8351 (tt0) cc_final: 0.7783 (tm-30) REVERT: A 594 ARG cc_start: 0.7422 (ttm110) cc_final: 0.7184 (mtm-85) REVERT: A 618 ILE cc_start: 0.8728 (mm) cc_final: 0.8523 (tp) REVERT: B 96 MET cc_start: 0.8340 (tmm) cc_final: 0.7858 (mtm) REVERT: B 130 MET cc_start: 0.7145 (mmt) cc_final: 0.6430 (mmt) REVERT: B 209 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6380 (mttp) REVERT: B 213 CYS cc_start: 0.8619 (t) cc_final: 0.8146 (t) REVERT: B 228 HIS cc_start: 0.6369 (m-70) cc_final: 0.5127 (p-80) REVERT: B 261 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7536 (tm-30) REVERT: B 294 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 301 LYS cc_start: 0.7913 (mtpp) cc_final: 0.7411 (mtmt) REVERT: B 315 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7864 (mp0) REVERT: B 339 TYR cc_start: 0.6985 (t80) cc_final: 0.6679 (t80) REVERT: B 345 MET cc_start: 0.7982 (mmp) cc_final: 0.6835 (ttp) REVERT: B 434 PHE cc_start: 0.8071 (m-80) cc_final: 0.7451 (t80) REVERT: B 440 MET cc_start: 0.8201 (tmm) cc_final: 0.7661 (tpp) REVERT: B 483 GLN cc_start: 0.7001 (tt0) cc_final: 0.6596 (mp10) REVERT: B 491 MET cc_start: 0.7001 (mmm) cc_final: 0.6582 (ttp) REVERT: B 519 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6088 (mp0) REVERT: B 546 ASN cc_start: 0.8133 (t0) cc_final: 0.7726 (t0) REVERT: B 567 THR cc_start: 0.7035 (m) cc_final: 0.6803 (m) REVERT: B 583 TRP cc_start: 0.7198 (t60) cc_final: 0.6834 (t60) REVERT: B 591 GLU cc_start: 0.8210 (tt0) cc_final: 0.7824 (tm-30) REVERT: B 618 ILE cc_start: 0.8807 (mm) cc_final: 0.8537 (tp) REVERT: C 130 MET cc_start: 0.7054 (mmt) cc_final: 0.6242 (mmt) REVERT: C 188 ASP cc_start: 0.7744 (t0) cc_final: 0.7307 (p0) REVERT: C 222 TYR cc_start: 0.8335 (m-80) cc_final: 0.7643 (m-80) REVERT: C 228 HIS cc_start: 0.6143 (m-70) cc_final: 0.4982 (p-80) REVERT: C 261 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7914 (tm-30) REVERT: C 301 LYS cc_start: 0.7560 (mtmt) cc_final: 0.7322 (mmtt) REVERT: C 315 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7845 (mp0) REVERT: C 339 TYR cc_start: 0.6968 (t80) cc_final: 0.6738 (t80) REVERT: C 434 PHE cc_start: 0.8139 (m-80) cc_final: 0.7473 (t80) REVERT: C 439 THR cc_start: 0.7814 (t) cc_final: 0.7467 (m) REVERT: C 483 GLN cc_start: 0.6809 (tt0) cc_final: 0.6396 (mp10) REVERT: C 528 MET cc_start: 0.7654 (tmm) cc_final: 0.7076 (tmm) REVERT: C 546 ASN cc_start: 0.8228 (t0) cc_final: 0.7810 (t0) REVERT: C 591 GLU cc_start: 0.8202 (tt0) cc_final: 0.7637 (tm-30) REVERT: C 594 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7081 (mtp-110) REVERT: C 616 SER cc_start: 0.8771 (t) cc_final: 0.7890 (p) REVERT: D 130 MET cc_start: 0.7440 (tpt) cc_final: 0.7006 (mmt) REVERT: D 173 VAL cc_start: 0.7779 (m) cc_final: 0.7565 (m) REVERT: D 215 MET cc_start: 0.8704 (tpp) cc_final: 0.8432 (mtt) REVERT: D 222 TYR cc_start: 0.8406 (m-80) cc_final: 0.7598 (m-80) REVERT: D 228 HIS cc_start: 0.6471 (m-70) cc_final: 0.5293 (p-80) REVERT: D 261 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7688 (tm-30) REVERT: D 315 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: D 434 PHE cc_start: 0.8104 (m-80) cc_final: 0.7464 (t80) REVERT: D 439 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7783 (m) REVERT: D 483 GLN cc_start: 0.6747 (tt0) cc_final: 0.6380 (mp10) REVERT: D 528 MET cc_start: 0.7120 (tpp) cc_final: 0.6788 (tpp) REVERT: D 538 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6451 (mp) REVERT: D 546 ASN cc_start: 0.7922 (t0) cc_final: 0.7471 (t0) REVERT: D 583 TRP cc_start: 0.7342 (t60) cc_final: 0.6907 (t60) REVERT: D 591 GLU cc_start: 0.8371 (tt0) cc_final: 0.7902 (tm-30) REVERT: D 594 ARG cc_start: 0.7395 (ttm110) cc_final: 0.6928 (mtp-110) outliers start: 57 outliers final: 41 residues processed: 519 average time/residue: 0.2854 time to fit residues: 232.7699 Evaluate side-chains 520 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 472 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 426 HIS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 426 HIS Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 426 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 472 PHE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 185 HIS A 257 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 197 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 185 HIS ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.150175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121855 restraints weight = 37685.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123280 restraints weight = 24377.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123576 restraints weight = 20440.211| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.7799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19484 Z= 0.221 Angle : 0.825 15.050 26440 Z= 0.381 Chirality : 0.045 0.335 3012 Planarity : 0.004 0.033 3336 Dihedral : 4.980 52.479 2598 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.81 % Allowed : 28.10 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2356 helix: 1.03 (0.14), residues: 1392 sheet: -2.23 (0.52), residues: 56 loop : -2.20 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 613 HIS 0.007 0.001 HIS D 522 PHE 0.039 0.002 PHE A 553 TYR 0.025 0.002 TYR D 339 ARG 0.007 0.000 ARG B 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4743.15 seconds wall clock time: 93 minutes 9.61 seconds (5589.61 seconds total)