Starting phenix.real_space_refine on Sat Feb 17 14:52:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/02_2024/6d7s_7824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/02_2024/6d7s_7824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/02_2024/6d7s_7824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/02_2024/6d7s_7824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/02_2024/6d7s_7824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d7s_7824/02_2024/6d7s_7824.pdb" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12280 2.51 5 N 3218 2.21 5 O 3364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 621": "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 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 621": "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 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 621": "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 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "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-5238/modules/chem_data/mon_lib" Total number of atoms: 19018 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "B" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4753 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Unresolved chain links: 2 Chain breaks: 1 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4755 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Time building chain proxies: 9.85, per 1000 atoms: 0.52 Number of scatterers: 19018 At special positions: 0 Unit cell: (136.22, 136.22, 121.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3364 8.00 N 3218 7.00 C 12280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.42 Conformation dependent library (CDL) restraints added in 3.6 seconds 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 8 sheets defined 62.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.609A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.559A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.739A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.737A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 removed outlier: 3.794A pdb=" N THR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.562A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.605A pdb=" N ARG A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.925A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.602A pdb=" N LEU A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.819A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.608A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 57 through 65 removed outlier: 3.559A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.740A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 342 removed outlier: 3.556A pdb=" N ILE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 346 No H-bonds generated for 'chain 'B' and resid 345 through 346' Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 removed outlier: 3.795A pdb=" N THR B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.562A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 removed outlier: 3.605A pdb=" N ARG B 470 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 4.381A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.924A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.602A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 567 removed outlier: 3.820A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.609A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.560A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.578A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.561A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.683A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.567A pdb=" N PHE C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.928A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.740A pdb=" N LEU C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 4.287A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.565A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 445 removed outlier: 3.794A pdb=" N THR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.561A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.604A pdb=" N ARG C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.924A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.345A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.603A pdb=" N LEU C 530 " --> pdb=" O TYR C 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 567 removed outlier: 3.819A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 587 removed outlier: 3.628A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.608A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.560A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.579A pdb=" N ALA D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.562A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.682A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.667A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.568A pdb=" N PHE D 152 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.929A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.739A pdb=" N LEU D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.537A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 removed outlier: 4.288A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.566A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.619A pdb=" N THR D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.687A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.992A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 346 removed outlier: 3.555A pdb=" N ILE D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.736A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 445 removed outlier: 3.795A pdb=" N THR D 431 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.561A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 472 removed outlier: 3.604A pdb=" N ARG D 470 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 4.380A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.925A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.346A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.603A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 removed outlier: 3.820A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 587 removed outlier: 3.627A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.561A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA4, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AA6, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.843A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'D' and resid 276 through 278 removed outlier: 3.844A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6085 1.34 - 1.46: 4458 1.46 - 1.58: 8641 1.58 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 19448 Sorted by residual: bond pdb=" C GLU C 164 " pdb=" N HIS C 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.42e+00 bond pdb=" C GLU A 164 " pdb=" N HIS A 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.34e+00 bond pdb=" C GLU B 164 " pdb=" N HIS B 165 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.32e+00 bond pdb=" C GLU D 164 " pdb=" N HIS D 165 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.27e+00 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.83e+00 ... (remaining 19443 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.36: 430 105.36 - 112.69: 10139 112.69 - 120.02: 7651 120.02 - 127.34: 7886 127.34 - 134.67: 280 Bond angle restraints: 26386 Sorted by residual: angle pdb=" C ASP D 223 " pdb=" N ARG D 224 " pdb=" CA ARG D 224 " ideal model delta sigma weight residual 120.54 129.35 -8.81 1.35e+00 5.49e-01 4.26e+01 angle pdb=" C ASP A 223 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " ideal model delta sigma weight residual 120.54 129.33 -8.79 1.35e+00 5.49e-01 4.24e+01 angle pdb=" C ASP C 223 " pdb=" N ARG C 224 " pdb=" CA ARG C 224 " ideal model delta sigma weight residual 120.54 129.31 -8.77 1.35e+00 5.49e-01 4.22e+01 angle pdb=" C ASP B 223 " pdb=" N ARG B 224 " pdb=" CA ARG B 224 " ideal model delta sigma weight residual 120.54 129.29 -8.75 1.35e+00 5.49e-01 4.20e+01 angle pdb=" N LEU D 612 " pdb=" CA LEU D 612 " pdb=" C LEU D 612 " ideal model delta sigma weight residual 114.56 106.46 8.10 1.27e+00 6.20e-01 4.06e+01 ... (remaining 26381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 10916 16.66 - 33.33: 584 33.33 - 49.99: 132 49.99 - 66.66: 8 66.66 - 83.32: 28 Dihedral angle restraints: 11668 sinusoidal: 4718 harmonic: 6950 Sorted by residual: dihedral pdb=" CA SER B 291 " pdb=" C SER B 291 " pdb=" N LEU B 292 " pdb=" CA LEU B 292 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER A 291 " pdb=" C SER A 291 " pdb=" N LEU A 292 " pdb=" CA LEU A 292 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER D 291 " pdb=" C SER D 291 " pdb=" N LEU D 292 " pdb=" CA LEU D 292 " ideal model delta harmonic sigma weight residual 180.00 150.87 29.13 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 11665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2189 0.057 - 0.114: 703 0.114 - 0.171: 94 0.171 - 0.228: 20 0.228 - 0.285: 4 Chirality restraints: 3010 Sorted by residual: chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3007 not shown) Planarity restraints: 3330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 353 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO A 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 353 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 354 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 353 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 354 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 354 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 354 " -0.036 5.00e-02 4.00e+02 ... (remaining 3327 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4620 2.78 - 3.31: 18427 3.31 - 3.84: 30816 3.84 - 4.37: 36892 4.37 - 4.90: 58694 Nonbonded interactions: 149449 Sorted by model distance: nonbonded pdb=" OD2 ASP B 279 " pdb=" OG1 THR B 281 " model vdw 2.248 2.440 nonbonded pdb=" OD2 ASP C 279 " pdb=" OG1 THR C 281 " model vdw 2.248 2.440 nonbonded pdb=" OD2 ASP A 279 " pdb=" OG1 THR A 281 " model vdw 2.248 2.440 nonbonded pdb=" OD2 ASP D 279 " pdb=" OG1 THR D 281 " model vdw 2.249 2.440 nonbonded pdb=" O ARG B 443 " pdb=" OG SER B 446 " model vdw 2.295 2.440 ... (remaining 149444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) selection = chain 'B' selection = (chain 'C' and (resid 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) selection = (chain 'D' and (resid 28 through 342 or (resid 343 and (name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 344 and (name CA or name C or name O or name CB or name OG1 or \ name CG2)) or resid 345 through 638)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.850 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 50.120 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 19448 Z= 0.460 Angle : 1.160 18.370 26386 Z= 0.640 Chirality : 0.056 0.285 3010 Planarity : 0.007 0.064 3330 Dihedral : 11.857 83.321 7168 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.07 % Favored : 87.76 % Rotamer: Outliers : 1.17 % Allowed : 2.33 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.61 (0.12), residues: 2353 helix: -3.58 (0.08), residues: 1298 sheet: -5.34 (0.26), residues: 40 loop : -3.75 (0.16), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 593 HIS 0.018 0.003 HIS C 522 PHE 0.034 0.003 PHE D 162 TYR 0.021 0.003 TYR A 524 ARG 0.007 0.001 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 717 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8094 (tptp) REVERT: A 92 LEU cc_start: 0.8365 (tp) cc_final: 0.7542 (tt) REVERT: A 200 LEU cc_start: 0.9531 (mt) cc_final: 0.9278 (mt) REVERT: A 245 LYS cc_start: 0.9265 (mtpt) cc_final: 0.8926 (tttt) REVERT: A 294 GLU cc_start: 0.8950 (tt0) cc_final: 0.8399 (pt0) REVERT: A 464 ASN cc_start: 0.8532 (t160) cc_final: 0.8208 (t160) REVERT: A 466 MET cc_start: 0.9212 (mmt) cc_final: 0.8840 (mmm) REVERT: A 475 LEU cc_start: 0.8907 (mp) cc_final: 0.8321 (tt) REVERT: A 485 MET cc_start: 0.9056 (mmp) cc_final: 0.8582 (mmp) REVERT: A 491 MET cc_start: 0.7738 (mmm) cc_final: 0.6913 (tpt) REVERT: A 578 MET cc_start: 0.9095 (mmt) cc_final: 0.8845 (mmt) REVERT: A 580 ASP cc_start: 0.9071 (t0) cc_final: 0.8669 (t0) REVERT: A 590 ASP cc_start: 0.8145 (p0) cc_final: 0.7928 (p0) REVERT: A 591 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8634 (mp0) REVERT: B 36 GLN cc_start: 0.7605 (tm130) cc_final: 0.7242 (tm-30) REVERT: B 63 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8155 (tptp) REVERT: B 92 LEU cc_start: 0.8353 (tp) cc_final: 0.6391 (tt) REVERT: B 245 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8890 (mttt) REVERT: B 280 LEU cc_start: 0.8969 (tp) cc_final: 0.8669 (tp) REVERT: B 389 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7264 (tp30) REVERT: B 455 SER cc_start: 0.9351 (m) cc_final: 0.9126 (p) REVERT: B 463 CYS cc_start: 0.8989 (m) cc_final: 0.8461 (t) REVERT: B 491 MET cc_start: 0.7778 (mmm) cc_final: 0.7118 (tpt) REVERT: B 508 PHE cc_start: 0.9134 (m-10) cc_final: 0.8741 (m-80) REVERT: B 520 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8672 (tp) REVERT: B 535 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 580 ASP cc_start: 0.8811 (t0) cc_final: 0.8609 (t0) REVERT: C 63 LYS cc_start: 0.8538 (ttpp) cc_final: 0.7677 (tptp) REVERT: C 92 LEU cc_start: 0.8599 (tp) cc_final: 0.8280 (pt) REVERT: C 130 MET cc_start: 0.6892 (tpp) cc_final: 0.6469 (tpp) REVERT: C 160 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8200 (pt) REVERT: C 209 LYS cc_start: 0.8453 (mttp) cc_final: 0.8079 (ptpt) REVERT: C 245 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8507 (tttt) REVERT: C 400 LEU cc_start: 0.9075 (mt) cc_final: 0.8367 (tt) REVERT: C 464 ASN cc_start: 0.8694 (t160) cc_final: 0.8383 (t0) REVERT: C 466 MET cc_start: 0.8944 (mmt) cc_final: 0.8511 (mmm) REVERT: C 485 MET cc_start: 0.8937 (mmp) cc_final: 0.8144 (mmp) REVERT: C 512 PHE cc_start: 0.8804 (m-10) cc_final: 0.8590 (m-80) REVERT: C 515 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7794 (tp30) REVERT: C 559 TYR cc_start: 0.8959 (t80) cc_final: 0.8610 (t80) REVERT: C 607 LYS cc_start: 0.8838 (mttp) cc_final: 0.8280 (mmmt) REVERT: D 63 LYS cc_start: 0.8510 (ttpp) cc_final: 0.7706 (tptp) REVERT: D 92 LEU cc_start: 0.8513 (tp) cc_final: 0.6755 (tt) REVERT: D 309 ASP cc_start: 0.8664 (m-30) cc_final: 0.8231 (m-30) REVERT: D 466 MET cc_start: 0.9266 (mmt) cc_final: 0.8624 (mmm) REVERT: D 485 MET cc_start: 0.8903 (mmp) cc_final: 0.8483 (mmp) REVERT: D 491 MET cc_start: 0.7280 (mmm) cc_final: 0.6855 (tpp) REVERT: D 591 GLU cc_start: 0.8943 (mt-10) cc_final: 0.7983 (mm-30) outliers start: 24 outliers final: 8 residues processed: 739 average time/residue: 0.3071 time to fit residues: 340.0480 Evaluate side-chains 452 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 442 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 165 HIS A 267 GLN A 365 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 73 HIS B 118 GLN B 165 HIS B 267 GLN B 426 HIS B 464 ASN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 165 HIS ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 548 ASN D 73 HIS D 118 GLN D 165 HIS D 267 GLN ** D 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19448 Z= 0.250 Angle : 0.776 13.388 26386 Z= 0.394 Chirality : 0.043 0.205 3010 Planarity : 0.005 0.054 3330 Dihedral : 6.463 28.215 2590 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 0.49 % Allowed : 3.69 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.15), residues: 2353 helix: -1.25 (0.13), residues: 1304 sheet: -5.32 (0.17), residues: 56 loop : -3.34 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 321 HIS 0.006 0.001 HIS C 426 PHE 0.027 0.002 PHE B 523 TYR 0.015 0.001 TYR C 559 ARG 0.007 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 542 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8430 (ttpp) cc_final: 0.8174 (tptp) REVERT: A 65 LEU cc_start: 0.8346 (mp) cc_final: 0.8006 (mp) REVERT: A 78 MET cc_start: 0.4890 (ptt) cc_final: 0.4532 (ptt) REVERT: A 130 MET cc_start: 0.7271 (tpp) cc_final: 0.6880 (mmt) REVERT: A 245 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8798 (tttt) REVERT: A 330 CYS cc_start: 0.9114 (m) cc_final: 0.8832 (m) REVERT: A 339 TYR cc_start: 0.9171 (t80) cc_final: 0.8600 (t80) REVERT: A 464 ASN cc_start: 0.8533 (t0) cc_final: 0.8317 (t0) REVERT: A 466 MET cc_start: 0.9248 (mmt) cc_final: 0.9004 (mmm) REVERT: A 497 MET cc_start: 0.6505 (mtp) cc_final: 0.6241 (mtp) REVERT: A 501 ILE cc_start: 0.9507 (mm) cc_final: 0.9202 (tp) REVERT: A 580 ASP cc_start: 0.9347 (t0) cc_final: 0.9026 (t0) REVERT: A 602 VAL cc_start: 0.9341 (m) cc_final: 0.9136 (p) REVERT: B 29 TRP cc_start: 0.7594 (p90) cc_final: 0.7289 (p90) REVERT: B 63 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8267 (tptp) REVERT: B 65 LEU cc_start: 0.8301 (mp) cc_final: 0.7990 (mp) REVERT: B 78 MET cc_start: 0.4944 (ptt) cc_final: 0.4714 (ptt) REVERT: B 92 LEU cc_start: 0.8425 (tp) cc_final: 0.7441 (tt) REVERT: B 110 MET cc_start: 0.8614 (mmm) cc_final: 0.8262 (mmm) REVERT: B 132 LEU cc_start: 0.9175 (mt) cc_final: 0.8912 (mt) REVERT: B 245 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8710 (mttt) REVERT: B 389 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7387 (tp30) REVERT: B 464 ASN cc_start: 0.8791 (t0) cc_final: 0.8485 (t0) REVERT: B 474 MET cc_start: 0.7384 (ptt) cc_final: 0.6903 (ptt) REVERT: B 478 PHE cc_start: 0.8651 (m-80) cc_final: 0.8403 (m-10) REVERT: B 481 MET cc_start: 0.8801 (mtp) cc_final: 0.8501 (mtm) REVERT: B 491 MET cc_start: 0.8068 (mmm) cc_final: 0.7419 (tpt) REVERT: B 535 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7460 (mt-10) REVERT: B 580 ASP cc_start: 0.8968 (t0) cc_final: 0.8749 (t0) REVERT: C 63 LYS cc_start: 0.8370 (ttpp) cc_final: 0.7824 (tptp) REVERT: C 67 TYR cc_start: 0.8358 (m-10) cc_final: 0.8147 (m-80) REVERT: C 110 MET cc_start: 0.8486 (mmm) cc_final: 0.8210 (mmm) REVERT: C 215 MET cc_start: 0.8165 (mpp) cc_final: 0.7873 (mpp) REVERT: C 232 LEU cc_start: 0.8814 (tp) cc_final: 0.8570 (tp) REVERT: C 245 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8336 (mttt) REVERT: C 400 LEU cc_start: 0.9193 (mt) cc_final: 0.8502 (tt) REVERT: C 428 LEU cc_start: 0.9478 (mp) cc_final: 0.9245 (mm) REVERT: C 464 ASN cc_start: 0.8860 (t0) cc_final: 0.8263 (t0) REVERT: C 466 MET cc_start: 0.9314 (mmt) cc_final: 0.8916 (mmm) REVERT: C 474 MET cc_start: 0.7426 (ptt) cc_final: 0.6661 (ptt) REVERT: C 475 LEU cc_start: 0.9202 (tp) cc_final: 0.8710 (tp) REVERT: C 485 MET cc_start: 0.9082 (mmp) cc_final: 0.8823 (mmp) REVERT: C 559 TYR cc_start: 0.9156 (t80) cc_final: 0.8542 (t80) REVERT: C 577 MET cc_start: 0.8526 (mmm) cc_final: 0.8246 (tpp) REVERT: C 591 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8259 (tm-30) REVERT: C 592 LEU cc_start: 0.9468 (mm) cc_final: 0.8724 (mm) REVERT: D 63 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7915 (tptp) REVERT: D 65 LEU cc_start: 0.8343 (mp) cc_final: 0.8079 (mp) REVERT: D 78 MET cc_start: 0.5245 (ptt) cc_final: 0.4850 (ptt) REVERT: D 92 LEU cc_start: 0.8369 (tp) cc_final: 0.7957 (tt) REVERT: D 96 MET cc_start: 0.9126 (mmm) cc_final: 0.8925 (mmm) REVERT: D 181 LEU cc_start: 0.9336 (mm) cc_final: 0.9129 (tp) REVERT: D 245 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8869 (tttt) REVERT: D 307 ILE cc_start: 0.9570 (mm) cc_final: 0.9331 (mm) REVERT: D 339 TYR cc_start: 0.9067 (t80) cc_final: 0.8611 (t80) REVERT: D 435 MET cc_start: 0.9220 (mmp) cc_final: 0.8928 (mmp) REVERT: D 442 MET cc_start: 0.8355 (ttm) cc_final: 0.8114 (ttm) REVERT: D 454 MET cc_start: 0.8896 (tpp) cc_final: 0.8682 (tpp) REVERT: D 466 MET cc_start: 0.9313 (mmt) cc_final: 0.9070 (mmt) REVERT: D 578 MET cc_start: 0.9180 (mmt) cc_final: 0.8975 (mmt) REVERT: D 591 GLU cc_start: 0.8768 (mt-10) cc_final: 0.7784 (mm-30) outliers start: 10 outliers final: 2 residues processed: 549 average time/residue: 0.2866 time to fit residues: 244.4366 Evaluate side-chains 390 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 388 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 206 GLN A 290 GLN A 365 ASN A 374 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 513 GLN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 257 GLN C 310 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN D 596 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19448 Z= 0.276 Angle : 0.765 13.010 26386 Z= 0.387 Chirality : 0.043 0.194 3010 Planarity : 0.005 0.061 3330 Dihedral : 6.108 27.368 2590 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 0.19 % Allowed : 3.89 % Favored : 95.92 % 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: -2.32 (0.16), residues: 2353 helix: -0.27 (0.14), residues: 1320 sheet: -5.01 (0.23), residues: 56 loop : -3.17 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 593 HIS 0.006 0.001 HIS B 522 PHE 0.028 0.002 PHE C 162 TYR 0.017 0.002 TYR B 559 ARG 0.007 0.001 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 466 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8173 (tptp) REVERT: A 66 LYS cc_start: 0.8047 (mppt) cc_final: 0.7641 (pptt) REVERT: A 78 MET cc_start: 0.4891 (ptt) cc_final: 0.4680 (ptt) REVERT: A 110 MET cc_start: 0.8736 (mmm) cc_final: 0.8395 (mmm) REVERT: A 209 LYS cc_start: 0.8830 (mttt) cc_final: 0.8619 (mttt) REVERT: A 245 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8778 (tttt) REVERT: A 330 CYS cc_start: 0.9248 (m) cc_final: 0.8928 (m) REVERT: A 339 TYR cc_start: 0.9098 (t80) cc_final: 0.8563 (t80) REVERT: A 463 CYS cc_start: 0.9038 (m) cc_final: 0.8707 (t) REVERT: A 464 ASN cc_start: 0.8872 (t0) cc_final: 0.8296 (t0) REVERT: A 501 ILE cc_start: 0.9566 (mm) cc_final: 0.9328 (tp) REVERT: A 535 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8300 (mt-10) REVERT: A 570 MET cc_start: 0.8718 (tpt) cc_final: 0.8454 (tpt) REVERT: A 574 LEU cc_start: 0.9564 (tt) cc_final: 0.9124 (tt) REVERT: A 575 ILE cc_start: 0.9593 (tt) cc_final: 0.9314 (tt) REVERT: A 578 MET cc_start: 0.8854 (mpp) cc_final: 0.8367 (mpp) REVERT: A 580 ASP cc_start: 0.9240 (t0) cc_final: 0.8975 (t0) REVERT: B 63 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8222 (tptp) REVERT: B 66 LYS cc_start: 0.8082 (mppt) cc_final: 0.7562 (pptt) REVERT: B 78 MET cc_start: 0.4918 (ptt) cc_final: 0.4692 (ptt) REVERT: B 110 MET cc_start: 0.8682 (mmm) cc_final: 0.8404 (mmm) REVERT: B 232 LEU cc_start: 0.8971 (tp) cc_final: 0.8761 (tp) REVERT: B 245 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8728 (mttt) REVERT: B 389 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7514 (tp30) REVERT: B 464 ASN cc_start: 0.9040 (t0) cc_final: 0.8732 (t0) REVERT: B 481 MET cc_start: 0.8882 (mtp) cc_final: 0.8633 (mtp) REVERT: B 491 MET cc_start: 0.8034 (mmm) cc_final: 0.7512 (tpt) REVERT: B 535 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 580 ASP cc_start: 0.8879 (t0) cc_final: 0.8582 (t0) REVERT: C 63 LYS cc_start: 0.8470 (ttpp) cc_final: 0.7824 (tptp) REVERT: C 110 MET cc_start: 0.8517 (mmm) cc_final: 0.8307 (mmm) REVERT: C 245 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8468 (mttt) REVERT: C 428 LEU cc_start: 0.9522 (mp) cc_final: 0.9274 (mm) REVERT: C 464 ASN cc_start: 0.9009 (t0) cc_final: 0.8517 (t0) REVERT: C 466 MET cc_start: 0.9391 (mmt) cc_final: 0.9085 (mmm) REVERT: C 491 MET cc_start: 0.8264 (tpt) cc_final: 0.7967 (tpp) REVERT: C 522 HIS cc_start: 0.8725 (m-70) cc_final: 0.8513 (m-70) REVERT: C 559 TYR cc_start: 0.9229 (t80) cc_final: 0.8670 (t80) REVERT: C 577 MET cc_start: 0.8731 (mmm) cc_final: 0.8240 (tpp) REVERT: C 591 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8220 (tm-30) REVERT: C 592 LEU cc_start: 0.9531 (mm) cc_final: 0.8774 (mm) REVERT: D 63 LYS cc_start: 0.8363 (ttpp) cc_final: 0.7929 (tptp) REVERT: D 78 MET cc_start: 0.5146 (ptt) cc_final: 0.4738 (ptt) REVERT: D 181 LEU cc_start: 0.9335 (mm) cc_final: 0.9104 (tp) REVERT: D 206 GLN cc_start: 0.8886 (mm110) cc_final: 0.8207 (tm-30) REVERT: D 245 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8877 (tttt) REVERT: D 339 TYR cc_start: 0.9020 (t80) cc_final: 0.8541 (t80) REVERT: D 437 LEU cc_start: 0.9340 (mp) cc_final: 0.8678 (mt) REVERT: D 454 MET cc_start: 0.9034 (tpp) cc_final: 0.8806 (tpp) REVERT: D 492 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8260 (mtp-110) REVERT: D 501 ILE cc_start: 0.9148 (tt) cc_final: 0.8934 (tp) REVERT: D 559 TYR cc_start: 0.9515 (t80) cc_final: 0.9179 (t80) REVERT: D 577 MET cc_start: 0.9351 (tpp) cc_final: 0.8933 (tpp) REVERT: D 590 ASP cc_start: 0.7954 (p0) cc_final: 0.7561 (p0) REVERT: D 591 GLU cc_start: 0.8792 (mt-10) cc_final: 0.7816 (mm-30) outliers start: 4 outliers final: 1 residues processed: 470 average time/residue: 0.2846 time to fit residues: 208.7562 Evaluate side-chains 359 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 358 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 20.0000 chunk 161 optimal weight: 0.3980 chunk 111 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 596 GLN B 206 GLN B 464 ASN ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19448 Z= 0.274 Angle : 0.734 14.076 26386 Z= 0.369 Chirality : 0.042 0.171 3010 Planarity : 0.004 0.049 3330 Dihedral : 5.858 25.035 2590 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 0.19 % Allowed : 3.94 % Favored : 95.87 % 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: -1.90 (0.17), residues: 2353 helix: 0.18 (0.14), residues: 1325 sheet: -4.68 (0.28), residues: 56 loop : -3.20 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 29 HIS 0.006 0.001 HIS D 258 PHE 0.031 0.002 PHE C 523 TYR 0.015 0.001 TYR B 559 ARG 0.008 0.001 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 468 time to evaluate : 2.166 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8286 (tptp) REVERT: A 78 MET cc_start: 0.4941 (ptt) cc_final: 0.4669 (ptt) REVERT: A 110 MET cc_start: 0.8748 (mmm) cc_final: 0.8435 (mmm) REVERT: A 209 LYS cc_start: 0.8779 (mttt) cc_final: 0.8526 (mttt) REVERT: A 245 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8878 (tttt) REVERT: A 330 CYS cc_start: 0.9276 (m) cc_final: 0.9059 (m) REVERT: A 339 TYR cc_start: 0.9138 (t80) cc_final: 0.8589 (t80) REVERT: A 464 ASN cc_start: 0.8812 (t0) cc_final: 0.8589 (t0) REVERT: A 535 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8433 (mt-10) REVERT: A 541 ILE cc_start: 0.9492 (mm) cc_final: 0.9060 (mm) REVERT: A 574 LEU cc_start: 0.9546 (tt) cc_final: 0.8932 (tt) REVERT: A 575 ILE cc_start: 0.9539 (tt) cc_final: 0.9216 (tt) REVERT: A 578 MET cc_start: 0.8708 (mpp) cc_final: 0.8301 (mpp) REVERT: A 580 ASP cc_start: 0.9233 (t0) cc_final: 0.8997 (t0) REVERT: A 588 GLU cc_start: 0.7070 (mp0) cc_final: 0.6724 (mp0) REVERT: B 29 TRP cc_start: 0.7654 (p90) cc_final: 0.7401 (p90) REVERT: B 63 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8337 (tptp) REVERT: B 78 MET cc_start: 0.5099 (ptt) cc_final: 0.4828 (ptt) REVERT: B 110 MET cc_start: 0.8706 (mmm) cc_final: 0.8448 (mmm) REVERT: B 232 LEU cc_start: 0.8995 (tp) cc_final: 0.8789 (tp) REVERT: B 245 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8809 (mttt) REVERT: B 389 GLU cc_start: 0.8759 (mt-10) cc_final: 0.7739 (tp30) REVERT: B 485 MET cc_start: 0.9058 (mmt) cc_final: 0.8747 (mmp) REVERT: B 491 MET cc_start: 0.8075 (mmm) cc_final: 0.7722 (tpt) REVERT: B 497 MET cc_start: 0.7277 (ttp) cc_final: 0.6948 (ttp) REVERT: B 535 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7288 (mt-10) REVERT: B 577 MET cc_start: 0.8506 (ttm) cc_final: 0.7748 (ttm) REVERT: B 580 ASP cc_start: 0.8947 (t0) cc_final: 0.8688 (t0) REVERT: C 29 TRP cc_start: 0.7799 (p90) cc_final: 0.7536 (p90) REVERT: C 63 LYS cc_start: 0.8485 (ttpp) cc_final: 0.7895 (tptp) REVERT: C 110 MET cc_start: 0.8519 (mmm) cc_final: 0.8313 (mmm) REVERT: C 113 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7659 (tp30) REVERT: C 245 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8622 (mttt) REVERT: C 330 CYS cc_start: 0.9106 (m) cc_final: 0.8662 (m) REVERT: C 331 MET cc_start: 0.8243 (mtm) cc_final: 0.6814 (mmt) REVERT: C 428 LEU cc_start: 0.9600 (mp) cc_final: 0.9036 (mm) REVERT: C 464 ASN cc_start: 0.9016 (t0) cc_final: 0.8519 (t0) REVERT: C 466 MET cc_start: 0.9387 (mmt) cc_final: 0.9076 (mmm) REVERT: C 485 MET cc_start: 0.8971 (mmt) cc_final: 0.8716 (mmp) REVERT: C 491 MET cc_start: 0.8249 (tpt) cc_final: 0.7993 (tpp) REVERT: C 493 PHE cc_start: 0.8828 (t80) cc_final: 0.8532 (t80) REVERT: C 559 TYR cc_start: 0.9390 (t80) cc_final: 0.8994 (t80) REVERT: C 591 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8252 (tm-30) REVERT: D 63 LYS cc_start: 0.8374 (ttpp) cc_final: 0.7716 (tptp) REVERT: D 78 MET cc_start: 0.5345 (ptt) cc_final: 0.4849 (ptt) REVERT: D 181 LEU cc_start: 0.9378 (mm) cc_final: 0.9161 (tp) REVERT: D 245 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8841 (mttt) REVERT: D 339 TYR cc_start: 0.9062 (t80) cc_final: 0.8639 (t80) REVERT: D 437 LEU cc_start: 0.9295 (mp) cc_final: 0.8692 (mt) REVERT: D 466 MET cc_start: 0.9443 (mmt) cc_final: 0.9213 (mmm) REVERT: D 485 MET cc_start: 0.9057 (mmp) cc_final: 0.8833 (mmp) REVERT: D 491 MET cc_start: 0.8057 (ttp) cc_final: 0.7351 (tpp) REVERT: D 559 TYR cc_start: 0.9523 (t80) cc_final: 0.8769 (t80) outliers start: 4 outliers final: 0 residues processed: 471 average time/residue: 0.2952 time to fit residues: 218.3841 Evaluate side-chains 357 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 206 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 118 GLN B 464 ASN B 546 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19448 Z= 0.195 Angle : 0.702 12.958 26386 Z= 0.347 Chirality : 0.042 0.301 3010 Planarity : 0.004 0.060 3330 Dihedral : 5.666 26.419 2590 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % 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: -1.54 (0.17), residues: 2353 helix: 0.51 (0.14), residues: 1331 sheet: -4.43 (0.32), residues: 56 loop : -3.14 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 593 HIS 0.012 0.001 HIS B 522 PHE 0.031 0.002 PHE A 434 TYR 0.013 0.001 TYR B 559 ARG 0.009 0.000 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 463 time to evaluate : 2.180 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8232 (tptp) REVERT: A 66 LYS cc_start: 0.8216 (mppt) cc_final: 0.7712 (pptt) REVERT: A 110 MET cc_start: 0.8712 (mmm) cc_final: 0.8411 (mmm) REVERT: A 209 LYS cc_start: 0.8725 (mttt) cc_final: 0.8519 (mttt) REVERT: A 245 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8893 (tttt) REVERT: A 339 TYR cc_start: 0.9116 (t80) cc_final: 0.8587 (t80) REVERT: A 464 ASN cc_start: 0.8762 (t0) cc_final: 0.8470 (t0) REVERT: A 554 MET cc_start: 0.8152 (tpt) cc_final: 0.7940 (tpt) REVERT: A 574 LEU cc_start: 0.9473 (tt) cc_final: 0.9128 (tt) REVERT: A 578 MET cc_start: 0.8812 (mpp) cc_final: 0.8264 (mpp) REVERT: A 580 ASP cc_start: 0.9224 (t0) cc_final: 0.9011 (t0) REVERT: A 587 HIS cc_start: 0.7738 (t70) cc_final: 0.7088 (m-70) REVERT: A 588 GLU cc_start: 0.6986 (mp0) cc_final: 0.6342 (mp0) REVERT: A 590 ASP cc_start: 0.7841 (p0) cc_final: 0.7427 (p0) REVERT: A 591 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8361 (mp0) REVERT: B 63 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8318 (tptp) REVERT: B 66 LYS cc_start: 0.8226 (mppt) cc_final: 0.7603 (pptt) REVERT: B 78 MET cc_start: 0.5178 (ptt) cc_final: 0.4944 (ptt) REVERT: B 336 TYR cc_start: 0.9329 (t80) cc_final: 0.9104 (t80) REVERT: B 389 GLU cc_start: 0.8761 (mt-10) cc_final: 0.7709 (tp30) REVERT: B 464 ASN cc_start: 0.9033 (t0) cc_final: 0.8525 (t0) REVERT: B 485 MET cc_start: 0.9067 (mmt) cc_final: 0.8821 (mmp) REVERT: B 491 MET cc_start: 0.8012 (mmm) cc_final: 0.7784 (tpt) REVERT: B 497 MET cc_start: 0.7299 (ttp) cc_final: 0.6997 (ttp) REVERT: B 577 MET cc_start: 0.8563 (ttm) cc_final: 0.7810 (ttm) REVERT: B 580 ASP cc_start: 0.8929 (t0) cc_final: 0.8689 (t0) REVERT: C 29 TRP cc_start: 0.7771 (p90) cc_final: 0.7521 (p90) REVERT: C 63 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8027 (tptp) REVERT: C 113 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7582 (tp30) REVERT: C 245 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8643 (mttt) REVERT: C 330 CYS cc_start: 0.9098 (m) cc_final: 0.8071 (t) REVERT: C 331 MET cc_start: 0.8075 (mtm) cc_final: 0.6698 (mmt) REVERT: C 428 LEU cc_start: 0.9248 (mp) cc_final: 0.9035 (mm) REVERT: C 464 ASN cc_start: 0.8953 (t0) cc_final: 0.8521 (t0) REVERT: C 491 MET cc_start: 0.8258 (tpt) cc_final: 0.7974 (tpp) REVERT: C 590 ASP cc_start: 0.7731 (p0) cc_final: 0.7499 (p0) REVERT: C 591 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8087 (tm-30) REVERT: D 34 ASP cc_start: 0.8874 (m-30) cc_final: 0.7790 (t70) REVERT: D 63 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8039 (tptp) REVERT: D 78 MET cc_start: 0.5149 (ptt) cc_final: 0.4612 (ptt) REVERT: D 206 GLN cc_start: 0.8850 (mm110) cc_final: 0.8287 (tm-30) REVERT: D 245 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8888 (mttt) REVERT: D 339 TYR cc_start: 0.9053 (t80) cc_final: 0.8701 (t80) REVERT: D 437 LEU cc_start: 0.9304 (mp) cc_final: 0.8692 (mt) REVERT: D 491 MET cc_start: 0.8019 (ttp) cc_final: 0.7444 (tpp) REVERT: D 528 MET cc_start: 0.8833 (ttm) cc_final: 0.8372 (ttm) REVERT: D 559 TYR cc_start: 0.9513 (t80) cc_final: 0.9262 (t80) REVERT: D 570 MET cc_start: 0.8577 (tpt) cc_final: 0.8276 (tpt) REVERT: D 590 ASP cc_start: 0.7804 (p0) cc_final: 0.7452 (p0) REVERT: D 591 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7756 (mm-30) outliers start: 2 outliers final: 0 residues processed: 464 average time/residue: 0.2878 time to fit residues: 210.8986 Evaluate side-chains 366 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 228 optimal weight: 0.7980 chunk 189 optimal weight: 0.0170 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN B 464 ASN C 290 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19448 Z= 0.183 Angle : 0.704 14.085 26386 Z= 0.343 Chirality : 0.041 0.201 3010 Planarity : 0.004 0.043 3330 Dihedral : 5.525 26.290 2590 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % 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: -1.28 (0.17), residues: 2353 helix: 0.69 (0.14), residues: 1345 sheet: -4.22 (0.32), residues: 56 loop : -3.01 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 593 HIS 0.004 0.001 HIS B 522 PHE 0.027 0.002 PHE B 434 TYR 0.013 0.001 TYR C 339 ARG 0.011 0.000 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 465 time to evaluate : 2.384 Fit side-chains TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8274 (tptp) REVERT: A 66 LYS cc_start: 0.8272 (mppt) cc_final: 0.7740 (pptt) REVERT: A 339 TYR cc_start: 0.9147 (t80) cc_final: 0.8671 (t80) REVERT: A 528 MET cc_start: 0.8850 (ttm) cc_final: 0.8575 (ttm) REVERT: A 575 ILE cc_start: 0.9516 (tt) cc_final: 0.9274 (tt) REVERT: A 580 ASP cc_start: 0.9118 (t0) cc_final: 0.8868 (t0) REVERT: A 587 HIS cc_start: 0.7782 (t70) cc_final: 0.7193 (m-70) REVERT: A 588 GLU cc_start: 0.7007 (mp0) cc_final: 0.6326 (mp0) REVERT: A 590 ASP cc_start: 0.7788 (p0) cc_final: 0.7335 (p0) REVERT: A 591 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8310 (mp0) REVERT: B 63 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8440 (tptp) REVERT: B 78 MET cc_start: 0.5091 (ptt) cc_final: 0.4876 (ptt) REVERT: B 245 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8863 (mttt) REVERT: B 294 GLU cc_start: 0.8693 (tt0) cc_final: 0.8479 (tt0) REVERT: B 339 TYR cc_start: 0.8735 (t80) cc_final: 0.8528 (t80) REVERT: B 389 GLU cc_start: 0.8758 (mt-10) cc_final: 0.7776 (tp30) REVERT: B 497 MET cc_start: 0.7214 (ttp) cc_final: 0.6923 (ttp) REVERT: B 577 MET cc_start: 0.8444 (ttm) cc_final: 0.7787 (ttm) REVERT: B 590 ASP cc_start: 0.7567 (p0) cc_final: 0.7119 (p0) REVERT: B 591 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8249 (mp0) REVERT: C 29 TRP cc_start: 0.7789 (p90) cc_final: 0.7552 (p90) REVERT: C 63 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8002 (tptp) REVERT: C 113 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7544 (tp30) REVERT: C 245 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8603 (mttt) REVERT: C 330 CYS cc_start: 0.9071 (m) cc_final: 0.8060 (t) REVERT: C 331 MET cc_start: 0.8113 (mtm) cc_final: 0.6699 (mmt) REVERT: C 428 LEU cc_start: 0.9215 (mp) cc_final: 0.8964 (mm) REVERT: C 442 MET cc_start: 0.8514 (mtp) cc_final: 0.8289 (mtp) REVERT: C 464 ASN cc_start: 0.8928 (t0) cc_final: 0.8521 (t0) REVERT: C 491 MET cc_start: 0.8285 (tpt) cc_final: 0.7999 (tpp) REVERT: C 528 MET cc_start: 0.8656 (ttm) cc_final: 0.8319 (ttm) REVERT: C 559 TYR cc_start: 0.9253 (t80) cc_final: 0.8819 (t80) REVERT: C 572 ASN cc_start: 0.9112 (m-40) cc_final: 0.8711 (m-40) REVERT: C 590 ASP cc_start: 0.7675 (p0) cc_final: 0.7472 (p0) REVERT: C 591 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8059 (tm-30) REVERT: D 63 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8089 (tptp) REVERT: D 78 MET cc_start: 0.4923 (ptt) cc_final: 0.4498 (ptt) REVERT: D 245 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8862 (mttt) REVERT: D 339 TYR cc_start: 0.9098 (t80) cc_final: 0.8783 (t80) REVERT: D 437 LEU cc_start: 0.9250 (mp) cc_final: 0.8626 (mt) REVERT: D 464 ASN cc_start: 0.8911 (t0) cc_final: 0.8502 (t0) REVERT: D 491 MET cc_start: 0.7985 (ttp) cc_final: 0.7357 (tpp) REVERT: D 501 ILE cc_start: 0.9140 (tt) cc_final: 0.8938 (tp) REVERT: D 528 MET cc_start: 0.8836 (ttm) cc_final: 0.8290 (ttm) REVERT: D 559 TYR cc_start: 0.9497 (t80) cc_final: 0.9160 (t80) REVERT: D 580 ASP cc_start: 0.8651 (t70) cc_final: 0.8434 (t70) REVERT: D 590 ASP cc_start: 0.7800 (p0) cc_final: 0.7427 (p0) REVERT: D 591 GLU cc_start: 0.8695 (mt-10) cc_final: 0.7771 (mm-30) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.2810 time to fit residues: 202.7724 Evaluate side-chains 360 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 464 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN C 41 GLN C 118 GLN C 370 GLN C 548 ASN D 118 GLN ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19448 Z= 0.235 Angle : 0.734 13.937 26386 Z= 0.363 Chirality : 0.042 0.236 3010 Planarity : 0.004 0.043 3330 Dihedral : 5.562 27.897 2590 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.19 % Allowed : 1.41 % Favored : 98.40 % 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: -1.32 (0.17), residues: 2353 helix: 0.56 (0.14), residues: 1368 sheet: -3.80 (0.35), residues: 56 loop : -3.00 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 29 HIS 0.006 0.001 HIS B 522 PHE 0.042 0.002 PHE A 456 TYR 0.014 0.001 TYR B 559 ARG 0.013 0.001 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 466 time to evaluate : 1.994 Fit side-chains TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7559 (p90) cc_final: 0.7227 (p90) REVERT: A 63 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8371 (tptp) REVERT: A 66 LYS cc_start: 0.8334 (mppt) cc_final: 0.7886 (pptt) REVERT: A 209 LYS cc_start: 0.8687 (mttt) cc_final: 0.8481 (mttt) REVERT: A 245 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8936 (mttt) REVERT: A 339 TYR cc_start: 0.9130 (t80) cc_final: 0.8666 (t80) REVERT: A 530 LEU cc_start: 0.9536 (mp) cc_final: 0.9331 (mp) REVERT: A 535 GLU cc_start: 0.8890 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 580 ASP cc_start: 0.9060 (t0) cc_final: 0.8859 (t0) REVERT: A 588 GLU cc_start: 0.6912 (mp0) cc_final: 0.6566 (mp0) REVERT: B 63 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8361 (tptp) REVERT: B 66 LYS cc_start: 0.8308 (mppt) cc_final: 0.7625 (pptt) REVERT: B 232 LEU cc_start: 0.8976 (tp) cc_final: 0.8767 (tp) REVERT: B 245 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8865 (mttt) REVERT: B 294 GLU cc_start: 0.8800 (tt0) cc_final: 0.8563 (tt0) REVERT: B 330 CYS cc_start: 0.9307 (m) cc_final: 0.8402 (p) REVERT: B 389 GLU cc_start: 0.8778 (mt-10) cc_final: 0.7812 (tp30) REVERT: B 464 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8595 (t160) REVERT: B 491 MET cc_start: 0.7759 (tpt) cc_final: 0.7280 (tpp) REVERT: B 535 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 559 TYR cc_start: 0.9365 (t80) cc_final: 0.9126 (t80) REVERT: B 577 MET cc_start: 0.8342 (ttm) cc_final: 0.7683 (ttm) REVERT: C 29 TRP cc_start: 0.7799 (p90) cc_final: 0.7580 (p90) REVERT: C 63 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8036 (tptp) REVERT: C 113 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7616 (tp30) REVERT: C 245 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8613 (mttt) REVERT: C 330 CYS cc_start: 0.9106 (m) cc_final: 0.8078 (t) REVERT: C 331 MET cc_start: 0.8173 (mtm) cc_final: 0.6732 (mmt) REVERT: C 464 ASN cc_start: 0.8953 (t0) cc_final: 0.8576 (t0) REVERT: C 485 MET cc_start: 0.9172 (mmt) cc_final: 0.8937 (mmp) REVERT: C 491 MET cc_start: 0.8296 (tpt) cc_final: 0.8030 (tpp) REVERT: C 528 MET cc_start: 0.8716 (ttm) cc_final: 0.8368 (ttm) REVERT: C 572 ASN cc_start: 0.9160 (m-40) cc_final: 0.8760 (m-40) REVERT: C 580 ASP cc_start: 0.8417 (t70) cc_final: 0.8168 (t70) REVERT: C 590 ASP cc_start: 0.7710 (p0) cc_final: 0.7447 (p0) REVERT: C 591 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8033 (tm-30) REVERT: C 596 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8341 (tp40) REVERT: D 63 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8095 (tptp) REVERT: D 78 MET cc_start: 0.5066 (ptt) cc_final: 0.4610 (ptt) REVERT: D 206 GLN cc_start: 0.8829 (mm110) cc_final: 0.8264 (tm-30) REVERT: D 245 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8868 (mttt) REVERT: D 339 TYR cc_start: 0.9036 (t80) cc_final: 0.8670 (t80) REVERT: D 464 ASN cc_start: 0.8940 (t0) cc_final: 0.8343 (t0) REVERT: D 491 MET cc_start: 0.8238 (ttp) cc_final: 0.7482 (tpp) REVERT: D 501 ILE cc_start: 0.9184 (tt) cc_final: 0.8954 (tp) REVERT: D 528 MET cc_start: 0.8838 (ttm) cc_final: 0.8295 (ttm) REVERT: D 559 TYR cc_start: 0.9443 (t80) cc_final: 0.8632 (t80) REVERT: D 580 ASP cc_start: 0.8569 (t70) cc_final: 0.8302 (t70) REVERT: D 590 ASP cc_start: 0.7865 (p0) cc_final: 0.7430 (p0) REVERT: D 591 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8469 (mp0) outliers start: 4 outliers final: 0 residues processed: 466 average time/residue: 0.2763 time to fit residues: 201.0392 Evaluate side-chains 359 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 358 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 A 596 GLN B 40 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN C 118 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19448 Z= 0.228 Angle : 0.749 13.776 26386 Z= 0.369 Chirality : 0.042 0.199 3010 Planarity : 0.004 0.091 3330 Dihedral : 5.531 27.252 2590 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.10 % Allowed : 1.31 % Favored : 98.59 % 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: -1.30 (0.17), residues: 2353 helix: 0.57 (0.14), residues: 1368 sheet: -3.65 (0.38), residues: 56 loop : -2.99 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 29 HIS 0.007 0.001 HIS A 587 PHE 0.038 0.002 PHE A 456 TYR 0.014 0.001 TYR B 559 ARG 0.013 0.001 ARG D 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 456 time to evaluate : 2.354 Fit side-chains TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7623 (p90) cc_final: 0.7358 (p90) REVERT: A 63 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8379 (tptp) REVERT: A 66 LYS cc_start: 0.8310 (mppt) cc_final: 0.7869 (pptt) REVERT: A 245 LYS cc_start: 0.9211 (mtpt) cc_final: 0.8951 (mttt) REVERT: A 339 TYR cc_start: 0.9161 (t80) cc_final: 0.8709 (t80) REVERT: A 515 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8470 (tp30) REVERT: A 530 LEU cc_start: 0.9524 (mp) cc_final: 0.9311 (mm) REVERT: A 535 GLU cc_start: 0.8867 (mt-10) cc_final: 0.7280 (mt-10) REVERT: B 63 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8394 (tptp) REVERT: B 66 LYS cc_start: 0.8353 (mppt) cc_final: 0.7683 (pptt) REVERT: B 245 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8826 (mttt) REVERT: B 294 GLU cc_start: 0.8784 (tt0) cc_final: 0.8553 (tt0) REVERT: B 330 CYS cc_start: 0.9273 (m) cc_final: 0.8361 (p) REVERT: B 339 TYR cc_start: 0.8857 (t80) cc_final: 0.8595 (t80) REVERT: B 389 GLU cc_start: 0.8767 (mt-10) cc_final: 0.7841 (tp30) REVERT: B 464 ASN cc_start: 0.9031 (t160) cc_final: 0.8604 (t160) REVERT: B 478 PHE cc_start: 0.8491 (m-10) cc_final: 0.8234 (m-10) REVERT: B 491 MET cc_start: 0.7804 (tpt) cc_final: 0.7322 (tpp) REVERT: B 535 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 559 TYR cc_start: 0.9359 (t80) cc_final: 0.9133 (t80) REVERT: B 590 ASP cc_start: 0.7700 (p0) cc_final: 0.7373 (p0) REVERT: B 591 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8245 (mp0) REVERT: C 29 TRP cc_start: 0.7791 (p90) cc_final: 0.7586 (p90) REVERT: C 63 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8054 (tptp) REVERT: C 113 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7624 (tp30) REVERT: C 245 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8602 (mttt) REVERT: C 330 CYS cc_start: 0.9082 (m) cc_final: 0.8086 (t) REVERT: C 331 MET cc_start: 0.8150 (mtm) cc_final: 0.6716 (mmt) REVERT: C 464 ASN cc_start: 0.8904 (t0) cc_final: 0.8582 (t0) REVERT: C 489 ASP cc_start: 0.8378 (t0) cc_final: 0.6297 (t0) REVERT: C 491 MET cc_start: 0.8299 (tpt) cc_final: 0.8031 (tpp) REVERT: C 492 ARG cc_start: 0.8084 (ptm-80) cc_final: 0.7809 (ptm160) REVERT: C 528 MET cc_start: 0.8717 (ttm) cc_final: 0.8368 (ttm) REVERT: C 559 TYR cc_start: 0.9315 (t80) cc_final: 0.9029 (t80) REVERT: C 572 ASN cc_start: 0.9115 (m-40) cc_final: 0.8729 (m-40) REVERT: C 590 ASP cc_start: 0.7735 (p0) cc_final: 0.7422 (p0) REVERT: C 591 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8054 (tm-30) REVERT: D 29 TRP cc_start: 0.7559 (p90) cc_final: 0.7316 (p90) REVERT: D 63 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8083 (tptp) REVERT: D 339 TYR cc_start: 0.9040 (t80) cc_final: 0.8673 (t80) REVERT: D 435 MET cc_start: 0.9224 (mmt) cc_final: 0.8999 (mmp) REVERT: D 464 ASN cc_start: 0.8947 (t0) cc_final: 0.8381 (t0) REVERT: D 485 MET cc_start: 0.9177 (mmp) cc_final: 0.8279 (mmm) REVERT: D 491 MET cc_start: 0.8253 (ttp) cc_final: 0.7507 (tpp) REVERT: D 501 ILE cc_start: 0.9204 (tt) cc_final: 0.9000 (tp) REVERT: D 528 MET cc_start: 0.8827 (ttm) cc_final: 0.8267 (ttm) REVERT: D 578 MET cc_start: 0.8938 (mmm) cc_final: 0.8477 (mmm) REVERT: D 580 ASP cc_start: 0.8556 (t70) cc_final: 0.8275 (t70) REVERT: D 590 ASP cc_start: 0.7840 (p0) cc_final: 0.7431 (p0) REVERT: D 591 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8437 (mp0) outliers start: 2 outliers final: 0 residues processed: 457 average time/residue: 0.2668 time to fit residues: 192.1451 Evaluate side-chains 363 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 211 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 0.0980 chunk 139 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN A 596 GLN B 118 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 596 GLN C 206 GLN ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19448 Z= 0.182 Angle : 0.738 13.257 26386 Z= 0.358 Chirality : 0.042 0.226 3010 Planarity : 0.004 0.061 3330 Dihedral : 5.404 28.950 2590 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.10 % Allowed : 0.44 % Favored : 99.47 % 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: -1.11 (0.17), residues: 2353 helix: 0.80 (0.15), residues: 1331 sheet: -3.62 (0.40), residues: 56 loop : -2.88 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 462 HIS 0.004 0.001 HIS C 522 PHE 0.043 0.002 PHE A 456 TYR 0.012 0.001 TYR B 559 ARG 0.014 0.000 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 472 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7787 (p90) cc_final: 0.7479 (p90) REVERT: A 63 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8349 (tptp) REVERT: A 66 LYS cc_start: 0.8269 (mppt) cc_final: 0.7910 (pptt) REVERT: A 96 MET cc_start: 0.9191 (mmp) cc_final: 0.8841 (mmm) REVERT: A 245 LYS cc_start: 0.9120 (mtpt) cc_final: 0.8864 (mttt) REVERT: A 339 TYR cc_start: 0.9160 (t80) cc_final: 0.8694 (t80) REVERT: A 501 ILE cc_start: 0.9579 (mm) cc_final: 0.9361 (mm) REVERT: A 522 HIS cc_start: 0.8306 (m-70) cc_final: 0.8011 (m-70) REVERT: A 535 GLU cc_start: 0.8812 (mt-10) cc_final: 0.6649 (mt-10) REVERT: A 537 PHE cc_start: 0.9287 (t80) cc_final: 0.9056 (t80) REVERT: B 63 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8409 (tptp) REVERT: B 66 LYS cc_start: 0.8324 (mppt) cc_final: 0.7780 (pptt) REVERT: B 245 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8627 (mttt) REVERT: B 330 CYS cc_start: 0.9238 (m) cc_final: 0.8896 (m) REVERT: B 339 TYR cc_start: 0.8900 (t80) cc_final: 0.8597 (t80) REVERT: B 389 GLU cc_start: 0.8917 (mt-10) cc_final: 0.7901 (tp30) REVERT: B 491 MET cc_start: 0.7857 (tpt) cc_final: 0.7419 (tpp) REVERT: B 559 TYR cc_start: 0.9325 (t80) cc_final: 0.9091 (t80) REVERT: B 591 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8368 (mp0) REVERT: C 63 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8071 (tptp) REVERT: C 110 MET cc_start: 0.8466 (mmm) cc_final: 0.7805 (mmm) REVERT: C 245 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8626 (mttt) REVERT: C 330 CYS cc_start: 0.9043 (m) cc_final: 0.8038 (t) REVERT: C 331 MET cc_start: 0.8107 (mtm) cc_final: 0.6670 (mmt) REVERT: C 454 MET cc_start: 0.9005 (tpt) cc_final: 0.8803 (tpt) REVERT: C 464 ASN cc_start: 0.8818 (t0) cc_final: 0.8461 (t0) REVERT: C 485 MET cc_start: 0.9036 (mmp) cc_final: 0.8762 (mmp) REVERT: C 489 ASP cc_start: 0.7972 (t0) cc_final: 0.7547 (t70) REVERT: C 491 MET cc_start: 0.8258 (tpt) cc_final: 0.7988 (tpp) REVERT: C 492 ARG cc_start: 0.8123 (ptm-80) cc_final: 0.7873 (ptm160) REVERT: C 496 LEU cc_start: 0.9091 (mt) cc_final: 0.8775 (mp) REVERT: C 528 MET cc_start: 0.8630 (ttm) cc_final: 0.8283 (ttm) REVERT: C 530 LEU cc_start: 0.9582 (mm) cc_final: 0.9314 (mm) REVERT: C 572 ASN cc_start: 0.9055 (m-40) cc_final: 0.8717 (m-40) REVERT: C 577 MET cc_start: 0.7783 (ttm) cc_final: 0.7579 (ttm) REVERT: C 580 ASP cc_start: 0.8277 (t70) cc_final: 0.7983 (t70) REVERT: C 596 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8358 (tp40) REVERT: D 29 TRP cc_start: 0.7606 (p90) cc_final: 0.7394 (p90) REVERT: D 63 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8068 (tptp) REVERT: D 206 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8657 (tt0) REVERT: D 220 LEU cc_start: 0.9275 (mm) cc_final: 0.9074 (pp) REVERT: D 245 LYS cc_start: 0.9172 (mtpt) cc_final: 0.8791 (mttt) REVERT: D 339 TYR cc_start: 0.9045 (t80) cc_final: 0.8656 (t80) REVERT: D 435 MET cc_start: 0.9288 (mmt) cc_final: 0.9031 (mmp) REVERT: D 464 ASN cc_start: 0.8938 (t0) cc_final: 0.8304 (t0) REVERT: D 485 MET cc_start: 0.9182 (mmp) cc_final: 0.8235 (mmm) REVERT: D 491 MET cc_start: 0.8288 (ttp) cc_final: 0.7588 (tpp) REVERT: D 559 TYR cc_start: 0.9282 (t80) cc_final: 0.8955 (t80) REVERT: D 578 MET cc_start: 0.8876 (mmm) cc_final: 0.8401 (mmm) REVERT: D 580 ASP cc_start: 0.8534 (t70) cc_final: 0.8203 (t0) REVERT: D 590 ASP cc_start: 0.7718 (p0) cc_final: 0.7196 (p0) outliers start: 2 outliers final: 2 residues processed: 472 average time/residue: 0.2755 time to fit residues: 202.5449 Evaluate side-chains 375 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 373 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 155 optimal weight: 0.0060 chunk 235 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 199 optimal weight: 0.2980 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 464 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 206 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19448 Z= 0.184 Angle : 0.756 14.028 26386 Z= 0.365 Chirality : 0.042 0.220 3010 Planarity : 0.004 0.066 3330 Dihedral : 5.377 30.080 2590 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.15 (0.17), residues: 2353 helix: 0.69 (0.14), residues: 1353 sheet: -3.56 (0.44), residues: 56 loop : -2.86 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 462 HIS 0.004 0.001 HIS D 587 PHE 0.039 0.002 PHE A 456 TYR 0.012 0.001 TYR B 559 ARG 0.015 0.000 ARG A 606 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 343 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7793 (p90) cc_final: 0.7515 (p90) REVERT: A 63 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8377 (tptp) REVERT: A 96 MET cc_start: 0.9192 (mmp) cc_final: 0.8835 (mmm) REVERT: A 245 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8677 (mttt) REVERT: A 339 TYR cc_start: 0.9164 (t80) cc_final: 0.8682 (t80) REVERT: A 454 MET cc_start: 0.9083 (tpt) cc_final: 0.8878 (tpt) REVERT: A 485 MET cc_start: 0.9243 (mmp) cc_final: 0.9003 (mmm) REVERT: A 522 HIS cc_start: 0.8348 (m-70) cc_final: 0.8040 (m-70) REVERT: A 530 LEU cc_start: 0.9595 (mm) cc_final: 0.9239 (mm) REVERT: A 535 GLU cc_start: 0.8771 (mt-10) cc_final: 0.6742 (mt-10) REVERT: B 63 LYS cc_start: 0.8689 (ttpp) cc_final: 0.8444 (tptp) REVERT: B 78 MET cc_start: 0.4965 (ttt) cc_final: 0.4206 (tpp) REVERT: B 294 GLU cc_start: 0.8759 (tt0) cc_final: 0.8493 (tt0) REVERT: B 330 CYS cc_start: 0.9210 (m) cc_final: 0.8894 (m) REVERT: B 336 TYR cc_start: 0.9283 (t80) cc_final: 0.9044 (t80) REVERT: B 339 TYR cc_start: 0.8922 (t80) cc_final: 0.8615 (t80) REVERT: B 389 GLU cc_start: 0.8875 (mt-10) cc_final: 0.7904 (tp30) REVERT: B 400 LEU cc_start: 0.8884 (mt) cc_final: 0.8275 (tt) REVERT: B 464 ASN cc_start: 0.8974 (t0) cc_final: 0.8388 (t0) REVERT: B 491 MET cc_start: 0.7872 (tpt) cc_final: 0.7483 (tpp) REVERT: B 559 TYR cc_start: 0.9297 (t80) cc_final: 0.9080 (t80) REVERT: B 591 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8339 (mp0) REVERT: C 63 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8000 (tptp) REVERT: C 110 MET cc_start: 0.8328 (mmm) cc_final: 0.8091 (mmm) REVERT: C 245 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8553 (mttt) REVERT: C 330 CYS cc_start: 0.9022 (m) cc_final: 0.7992 (t) REVERT: C 331 MET cc_start: 0.8091 (mtm) cc_final: 0.6630 (mmt) REVERT: C 454 MET cc_start: 0.9010 (tpt) cc_final: 0.8638 (tpt) REVERT: C 464 ASN cc_start: 0.8972 (t0) cc_final: 0.8623 (t0) REVERT: C 489 ASP cc_start: 0.7974 (t0) cc_final: 0.7570 (t70) REVERT: C 492 ARG cc_start: 0.8184 (ptm-80) cc_final: 0.7923 (ptm160) REVERT: C 512 PHE cc_start: 0.8968 (m-80) cc_final: 0.8482 (m-80) REVERT: C 515 GLU cc_start: 0.7991 (tp30) cc_final: 0.7659 (mt-10) REVERT: C 528 MET cc_start: 0.8637 (ttm) cc_final: 0.8302 (ttm) REVERT: C 530 LEU cc_start: 0.9587 (mm) cc_final: 0.9296 (mm) REVERT: C 559 TYR cc_start: 0.9272 (t80) cc_final: 0.8959 (t80) REVERT: C 572 ASN cc_start: 0.8920 (m-40) cc_final: 0.8554 (m-40) REVERT: C 580 ASP cc_start: 0.8234 (t70) cc_final: 0.7966 (t70) REVERT: C 596 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8341 (tp40) REVERT: D 29 TRP cc_start: 0.7581 (p90) cc_final: 0.7330 (p90) REVERT: D 63 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8049 (tptp) REVERT: D 110 MET cc_start: 0.8353 (mmm) cc_final: 0.7875 (mmm) REVERT: D 245 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8712 (mttt) REVERT: D 339 TYR cc_start: 0.9040 (t80) cc_final: 0.8652 (t80) REVERT: D 464 ASN cc_start: 0.8920 (t0) cc_final: 0.8318 (t0) REVERT: D 485 MET cc_start: 0.9173 (mmp) cc_final: 0.8294 (mmm) REVERT: D 491 MET cc_start: 0.8318 (ttp) cc_final: 0.7568 (tpp) REVERT: D 530 LEU cc_start: 0.9521 (mm) cc_final: 0.9128 (mm) REVERT: D 559 TYR cc_start: 0.9248 (t80) cc_final: 0.8885 (t80) REVERT: D 578 MET cc_start: 0.8826 (mmm) cc_final: 0.8459 (mmm) REVERT: D 580 ASP cc_start: 0.8489 (t70) cc_final: 0.8168 (t0) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.2685 time to fit residues: 195.0746 Evaluate side-chains 361 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 192 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 464 ASN A 596 GLN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074942 restraints weight = 66604.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.077011 restraints weight = 39036.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078466 restraints weight = 26529.453| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19448 Z= 0.192 Angle : 0.758 13.825 26386 Z= 0.364 Chirality : 0.042 0.209 3010 Planarity : 0.004 0.059 3330 Dihedral : 5.290 30.097 2590 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.10 % Allowed : 0.44 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2353 helix: 0.68 (0.14), residues: 1366 sheet: -3.38 (0.48), residues: 56 loop : -2.87 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 462 HIS 0.005 0.001 HIS C 587 PHE 0.034 0.002 PHE A 434 TYR 0.013 0.001 TYR B 559 ARG 0.014 0.000 ARG A 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4418.60 seconds wall clock time: 80 minutes 43.72 seconds (4843.72 seconds total)