Starting phenix.real_space_refine on Mon Mar 18 15:59:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/03_2024/6pvp_20496.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/03_2024/6pvp_20496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/03_2024/6pvp_20496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/03_2024/6pvp_20496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/03_2024/6pvp_20496.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/03_2024/6pvp_20496.pdb" } resolution = 4.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 Na 1 4.78 5 C 13864 2.51 5 N 3548 2.21 5 O 3888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 375": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 375": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21425 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5356 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 640} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5356 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 640} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5356 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 640} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5356 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 640} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.69, per 1000 atoms: 0.50 Number of scatterers: 21425 At special positions: 0 Unit cell: (144.16, 143.1, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 Na 1 11.00 O 3888 8.00 N 3548 7.00 C 13864 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: 8.19 Conformation dependent library (CDL) restraints added in 3.8 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 4 sheets defined 62.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.324A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.538A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 4.199A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.028A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 4.232A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.520A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.825A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.566A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.616A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.515A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.534A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.689A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.717A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.507A pdb=" N LYS A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 503 removed outlier: 4.066A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.549A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 563 Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.557A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 591 removed outlier: 4.019A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 607 removed outlier: 4.106A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.804A pdb=" N SER A 620 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.652A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 668 through 687 removed outlier: 3.532A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.801A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 696 " --> pdb=" O TRP A 692 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.324A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.538A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.200A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.029A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 4.233A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.520A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.825A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 329 removed outlier: 3.565A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.615A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 334 " --> pdb=" O TRP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.515A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.534A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.690A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.716A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.508A pdb=" N LYS B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 503 removed outlier: 4.066A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 514 through 520 Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.548A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 563 Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.557A pdb=" N MET B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 591 removed outlier: 4.019A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 607 removed outlier: 4.107A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.804A pdb=" N SER B 620 " --> pdb=" O LYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.653A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.532A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.800A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 696 " --> pdb=" O TRP B 692 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 removed outlier: 4.324A pdb=" N ARG C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.538A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 4.201A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.030A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 4.233A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.519A pdb=" N LEU C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.826A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 329 removed outlier: 3.566A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.616A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 334 " --> pdb=" O TRP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.515A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.534A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.690A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.716A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 479 removed outlier: 3.508A pdb=" N LYS C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 503 removed outlier: 4.066A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' Processing helix chain 'C' and resid 514 through 520 Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.549A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 563 Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.557A pdb=" N MET C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 591 removed outlier: 4.019A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 607 removed outlier: 4.107A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.803A pdb=" N SER C 620 " --> pdb=" O LYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.652A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 Processing helix chain 'C' and resid 668 through 687 removed outlier: 3.532A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.801A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 696 " --> pdb=" O TRP C 692 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 130 removed outlier: 4.324A pdb=" N ARG D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.538A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 4.200A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.029A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 4.233A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.519A pdb=" N LEU D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.826A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.566A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.615A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D 334 " --> pdb=" O TRP D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.515A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 363 " --> pdb=" O TYR D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.534A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 removed outlier: 3.690A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.717A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 479 removed outlier: 3.508A pdb=" N LYS D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 503 removed outlier: 4.066A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 506 No H-bonds generated for 'chain 'D' and resid 504 through 506' Processing helix chain 'D' and resid 514 through 520 Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.550A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 531 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 563 Processing helix chain 'D' and resid 569 through 574 removed outlier: 3.557A pdb=" N MET D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 591 removed outlier: 4.019A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 607 removed outlier: 4.107A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 621 removed outlier: 3.804A pdb=" N SER D 620 " --> pdb=" O LYS D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.652A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU D 631 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 666 Processing helix chain 'D' and resid 668 through 687 removed outlier: 3.532A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.800A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 696 " --> pdb=" O TRP D 692 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 385 through 386 removed outlier: 3.521A pdb=" N SER A 386 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 385 through 386 removed outlier: 3.521A pdb=" N SER B 386 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 385 through 386 removed outlier: 3.521A pdb=" N SER C 386 " --> pdb=" O ASN C 735 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 385 through 386 removed outlier: 3.521A pdb=" N SER D 386 " --> pdb=" O ASN D 735 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2700 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: 5.95 Time building geometry restraints manager: 8.89 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: 6750 1.34 - 1.46: 4704 1.46 - 1.58: 10226 1.58 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 21884 Sorted by residual: bond pdb=" CA GLU A 687 " pdb=" CB GLU A 687 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.33e-02 5.65e+03 5.72e+00 bond pdb=" CA GLU D 687 " pdb=" CB GLU D 687 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.33e-02 5.65e+03 5.43e+00 bond pdb=" CA GLU B 687 " pdb=" CB GLU B 687 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.33e-02 5.65e+03 5.43e+00 bond pdb=" CA GLU C 687 " pdb=" CB GLU C 687 " ideal model delta sigma weight residual 1.524 1.493 0.030 1.33e-02 5.65e+03 5.21e+00 bond pdb=" C SER C 102 " pdb=" N PRO C 103 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.80e+00 ... (remaining 21879 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.36: 375 105.36 - 113.07: 11660 113.07 - 120.78: 10903 120.78 - 128.49: 6487 128.49 - 136.20: 207 Bond angle restraints: 29632 Sorted by residual: angle pdb=" C GLU D 418 " pdb=" N MET D 419 " pdb=" CA MET D 419 " ideal model delta sigma weight residual 121.54 133.44 -11.90 1.91e+00 2.74e-01 3.88e+01 angle pdb=" C GLN B 112 " pdb=" N ARG B 113 " pdb=" CA ARG B 113 " ideal model delta sigma weight residual 121.54 133.42 -11.88 1.91e+00 2.74e-01 3.87e+01 angle pdb=" C GLU A 418 " pdb=" N MET A 419 " pdb=" CA MET A 419 " ideal model delta sigma weight residual 121.54 133.41 -11.87 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C GLU C 418 " pdb=" N MET C 419 " pdb=" CA MET C 419 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C GLU B 418 " pdb=" N MET B 419 " pdb=" CA MET B 419 " ideal model delta sigma weight residual 121.54 133.39 -11.85 1.91e+00 2.74e-01 3.85e+01 ... (remaining 29627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 11959 15.54 - 31.08: 897 31.08 - 46.62: 236 46.62 - 62.17: 44 62.17 - 77.71: 20 Dihedral angle restraints: 13156 sinusoidal: 5344 harmonic: 7812 Sorted by residual: dihedral pdb=" CA VAL D 93 " pdb=" C VAL D 93 " pdb=" N THR D 94 " pdb=" CA THR D 94 " ideal model delta harmonic sigma weight residual 180.00 130.02 49.98 0 5.00e+00 4.00e-02 9.99e+01 dihedral pdb=" CA VAL A 93 " pdb=" C VAL A 93 " pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta harmonic sigma weight residual 180.00 130.02 49.98 0 5.00e+00 4.00e-02 9.99e+01 dihedral pdb=" CA VAL C 93 " pdb=" C VAL C 93 " pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta harmonic sigma weight residual 180.00 130.07 49.93 0 5.00e+00 4.00e-02 9.97e+01 ... (remaining 13153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1980 0.046 - 0.091: 1040 0.091 - 0.137: 273 0.137 - 0.183: 68 0.183 - 0.228: 23 Chirality restraints: 3384 Sorted by residual: chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL B 154 " pdb=" CA VAL B 154 " pdb=" CG1 VAL B 154 " pdb=" CG2 VAL B 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL C 154 " pdb=" CA VAL C 154 " pdb=" CG1 VAL C 154 " pdb=" CG2 VAL C 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 3381 not shown) Planarity restraints: 3724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 648 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C SER D 648 " -0.037 2.00e-02 2.50e+03 pdb=" O SER D 648 " 0.014 2.00e-02 2.50e+03 pdb=" N THR D 649 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 648 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C SER A 648 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 648 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 649 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 648 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C SER C 648 " 0.036 2.00e-02 2.50e+03 pdb=" O SER C 648 " -0.013 2.00e-02 2.50e+03 pdb=" N THR C 649 " -0.012 2.00e-02 2.50e+03 ... (remaining 3721 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4094 2.76 - 3.29: 21356 3.29 - 3.83: 35071 3.83 - 4.36: 39942 4.36 - 4.90: 63049 Nonbonded interactions: 163512 Sorted by model distance: nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR C 594 " pdb=" OG1 THR C 636 " model vdw 2.282 2.440 ... (remaining 163507 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 85 through 745) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.550 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 54.220 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.110 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 21884 Z= 0.496 Angle : 1.244 11.899 29632 Z= 0.659 Chirality : 0.058 0.228 3384 Planarity : 0.007 0.049 3724 Dihedral : 12.740 77.706 8076 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.63 % Favored : 84.22 % Rotamer: Outliers : 0.81 % Allowed : 10.59 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.94 % 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: -5.24 (0.12), residues: 2636 helix: -3.00 (0.09), residues: 1380 sheet: -5.09 (0.40), residues: 48 loop : -4.00 (0.15), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 739 HIS 0.015 0.002 HIS A 256 PHE 0.020 0.003 PHE D 728 TYR 0.018 0.003 TYR A 594 ARG 0.007 0.001 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 700 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.9372 (tttt) cc_final: 0.9053 (ptpt) REVERT: A 129 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7795 (tm-30) REVERT: A 169 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7821 (pttt) REVERT: A 210 GLU cc_start: 0.8754 (tt0) cc_final: 0.8238 (tm-30) REVERT: A 321 TYR cc_start: 0.8419 (t80) cc_final: 0.7938 (t80) REVERT: A 388 SER cc_start: 0.8637 (m) cc_final: 0.8234 (p) REVERT: A 512 ASP cc_start: 0.6174 (m-30) cc_final: 0.5837 (t0) REVERT: A 526 PHE cc_start: 0.8083 (m-10) cc_final: 0.7695 (m-10) REVERT: A 550 CYS cc_start: 0.8657 (t) cc_final: 0.8439 (t) REVERT: A 572 MET cc_start: 0.9133 (mmt) cc_final: 0.8250 (mmm) REVERT: A 578 MET cc_start: 0.8624 (mtp) cc_final: 0.8219 (mtp) REVERT: A 595 ILE cc_start: 0.8677 (mt) cc_final: 0.8332 (mt) REVERT: A 702 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 210 GLU cc_start: 0.8707 (tt0) cc_final: 0.8486 (pt0) REVERT: B 448 TYR cc_start: 0.8713 (t80) cc_final: 0.7542 (t80) REVERT: B 493 TRP cc_start: 0.7082 (m100) cc_final: 0.6192 (m100) REVERT: B 512 ASP cc_start: 0.6611 (m-30) cc_final: 0.6406 (t0) REVERT: B 526 PHE cc_start: 0.7799 (m-10) cc_final: 0.7445 (m-10) REVERT: B 550 CYS cc_start: 0.8742 (t) cc_final: 0.8480 (t) REVERT: B 572 MET cc_start: 0.9280 (mmt) cc_final: 0.8918 (mmm) REVERT: B 574 MET cc_start: 0.7762 (ppp) cc_final: 0.6460 (ppp) REVERT: B 578 MET cc_start: 0.8621 (mtp) cc_final: 0.7805 (mtt) REVERT: B 595 ILE cc_start: 0.8684 (mt) cc_final: 0.8446 (mt) REVERT: B 632 LEU cc_start: 0.9436 (mt) cc_final: 0.9183 (mm) REVERT: B 735 ASN cc_start: 0.7308 (m110) cc_final: 0.7099 (m110) REVERT: C 303 LEU cc_start: 0.9486 (mt) cc_final: 0.9202 (mp) REVERT: C 323 MET cc_start: 0.8450 (ttm) cc_final: 0.8165 (tpt) REVERT: C 388 SER cc_start: 0.8562 (m) cc_final: 0.8313 (p) REVERT: C 448 TYR cc_start: 0.8767 (t80) cc_final: 0.8561 (t80) REVERT: C 455 LEU cc_start: 0.9456 (tp) cc_final: 0.9254 (tp) REVERT: C 503 ILE cc_start: 0.8841 (mt) cc_final: 0.8598 (pt) REVERT: C 526 PHE cc_start: 0.7637 (m-10) cc_final: 0.7218 (m-80) REVERT: C 550 CYS cc_start: 0.8783 (t) cc_final: 0.8542 (t) REVERT: C 572 MET cc_start: 0.8917 (mmt) cc_final: 0.8624 (mmm) REVERT: C 574 MET cc_start: 0.7861 (ppp) cc_final: 0.6528 (ppp) REVERT: C 578 MET cc_start: 0.8796 (mtp) cc_final: 0.7697 (mtp) REVERT: C 597 PHE cc_start: 0.8307 (m-10) cc_final: 0.8101 (m-10) REVERT: C 632 LEU cc_start: 0.9439 (mt) cc_final: 0.9130 (mm) REVERT: D 120 LYS cc_start: 0.9344 (tttt) cc_final: 0.8950 (ptpt) REVERT: D 321 TYR cc_start: 0.8369 (t80) cc_final: 0.7965 (t80) REVERT: D 388 SER cc_start: 0.8629 (m) cc_final: 0.8361 (p) REVERT: D 440 MET cc_start: 0.8486 (mmt) cc_final: 0.8111 (mmp) REVERT: D 512 ASP cc_start: 0.5988 (m-30) cc_final: 0.5686 (t0) REVERT: D 526 PHE cc_start: 0.8080 (m-10) cc_final: 0.7734 (m-10) REVERT: D 566 THR cc_start: 0.9304 (p) cc_final: 0.9095 (t) REVERT: D 572 MET cc_start: 0.9019 (mmt) cc_final: 0.7997 (mmm) REVERT: D 574 MET cc_start: 0.8027 (ppp) cc_final: 0.6689 (tmm) REVERT: D 578 MET cc_start: 0.8872 (mtp) cc_final: 0.8381 (mtt) REVERT: D 635 LEU cc_start: 0.9199 (mt) cc_final: 0.8518 (mt) REVERT: D 702 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7592 (tm-30) outliers start: 19 outliers final: 3 residues processed: 712 average time/residue: 0.3423 time to fit residues: 365.6429 Evaluate side-chains 421 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 418 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN A 255 GLN ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN C 99 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 255 GLN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21884 Z= 0.205 Angle : 0.764 8.093 29632 Z= 0.396 Chirality : 0.041 0.168 3384 Planarity : 0.005 0.042 3724 Dihedral : 6.500 32.846 2864 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.24 % Favored : 86.46 % Rotamer: Outliers : 0.17 % Allowed : 4.34 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.35 (0.14), residues: 2636 helix: -1.13 (0.12), residues: 1456 sheet: -4.98 (0.38), residues: 48 loop : -3.63 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 739 HIS 0.004 0.001 HIS B 160 PHE 0.026 0.002 PHE A 124 TYR 0.013 0.001 TYR C 321 ARG 0.006 0.000 ARG D 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 605 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.9256 (tttt) cc_final: 0.9034 (ptpt) REVERT: A 173 MET cc_start: 0.8343 (mtm) cc_final: 0.7932 (mmt) REVERT: A 321 TYR cc_start: 0.8014 (t80) cc_final: 0.7719 (t80) REVERT: A 448 TYR cc_start: 0.8351 (t80) cc_final: 0.8135 (t80) REVERT: A 451 TYR cc_start: 0.8238 (t80) cc_final: 0.7819 (t80) REVERT: A 464 ARG cc_start: 0.7014 (ttt180) cc_final: 0.6589 (ttt180) REVERT: A 493 TRP cc_start: 0.6879 (m100) cc_final: 0.6642 (m100) REVERT: A 512 ASP cc_start: 0.6064 (m-30) cc_final: 0.5650 (t0) REVERT: A 550 CYS cc_start: 0.8772 (t) cc_final: 0.8553 (t) REVERT: A 557 LEU cc_start: 0.8965 (tt) cc_final: 0.8656 (tt) REVERT: A 574 MET cc_start: 0.8128 (ppp) cc_final: 0.7363 (ppp) REVERT: A 578 MET cc_start: 0.8351 (mtp) cc_final: 0.8049 (mtm) REVERT: A 702 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 124 PHE cc_start: 0.8215 (m-10) cc_final: 0.7997 (m-80) REVERT: B 159 MET cc_start: 0.8398 (mmt) cc_final: 0.7788 (mmt) REVERT: B 173 MET cc_start: 0.8446 (mtt) cc_final: 0.8222 (mmm) REVERT: B 271 CYS cc_start: 0.9363 (m) cc_final: 0.8697 (t) REVERT: B 388 SER cc_start: 0.8662 (m) cc_final: 0.7484 (p) REVERT: B 443 LEU cc_start: 0.9228 (tt) cc_final: 0.8844 (mm) REVERT: B 448 TYR cc_start: 0.8554 (t80) cc_final: 0.7741 (t80) REVERT: B 484 LEU cc_start: 0.8582 (tp) cc_final: 0.8375 (tp) REVERT: B 493 TRP cc_start: 0.7063 (m100) cc_final: 0.6173 (m100) REVERT: B 512 ASP cc_start: 0.6587 (m-30) cc_final: 0.6301 (t0) REVERT: B 574 MET cc_start: 0.7608 (ppp) cc_final: 0.6950 (ppp) REVERT: B 578 MET cc_start: 0.8645 (mtp) cc_final: 0.8364 (mtm) REVERT: B 687 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7531 (tm-30) REVERT: B 735 ASN cc_start: 0.6413 (m110) cc_final: 0.5926 (m110) REVERT: C 173 MET cc_start: 0.8288 (mmp) cc_final: 0.7573 (mmp) REVERT: C 388 SER cc_start: 0.8414 (m) cc_final: 0.7627 (p) REVERT: C 443 LEU cc_start: 0.9385 (tt) cc_final: 0.8982 (mm) REVERT: C 448 TYR cc_start: 0.8735 (t80) cc_final: 0.8313 (t80) REVERT: C 451 TYR cc_start: 0.8647 (t80) cc_final: 0.8406 (t80) REVERT: C 455 LEU cc_start: 0.9511 (tp) cc_final: 0.9234 (tp) REVERT: C 464 ARG cc_start: 0.6462 (mtt-85) cc_final: 0.5933 (ttt180) REVERT: C 529 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8875 (tm-30) REVERT: C 574 MET cc_start: 0.7755 (ppp) cc_final: 0.6977 (ppp) REVERT: C 578 MET cc_start: 0.8673 (mtp) cc_final: 0.8279 (mtm) REVERT: C 632 LEU cc_start: 0.9205 (mt) cc_final: 0.8918 (mm) REVERT: C 735 ASN cc_start: 0.7659 (m110) cc_final: 0.7331 (m110) REVERT: D 120 LYS cc_start: 0.9233 (tttt) cc_final: 0.8970 (ptpt) REVERT: D 134 GLU cc_start: 0.8653 (pm20) cc_final: 0.8425 (pm20) REVERT: D 156 ASP cc_start: 0.8981 (m-30) cc_final: 0.8778 (m-30) REVERT: D 173 MET cc_start: 0.8320 (mtm) cc_final: 0.8098 (mmt) REVERT: D 321 TYR cc_start: 0.8092 (t80) cc_final: 0.7744 (t80) REVERT: D 418 GLU cc_start: 0.8542 (mp0) cc_final: 0.8306 (mp0) REVERT: D 447 PHE cc_start: 0.8598 (m-80) cc_final: 0.8319 (m-80) REVERT: D 448 TYR cc_start: 0.8489 (t80) cc_final: 0.8279 (t80) REVERT: D 493 TRP cc_start: 0.7069 (m100) cc_final: 0.6024 (m100) REVERT: D 512 ASP cc_start: 0.5756 (m-30) cc_final: 0.5541 (t0) REVERT: D 529 GLN cc_start: 0.8712 (tp40) cc_final: 0.8510 (tp40) REVERT: D 553 LEU cc_start: 0.9333 (tt) cc_final: 0.9108 (pp) REVERT: D 557 LEU cc_start: 0.8961 (tt) cc_final: 0.8566 (tt) REVERT: D 574 MET cc_start: 0.7887 (ppp) cc_final: 0.7614 (ppp) REVERT: D 582 VAL cc_start: 0.9011 (t) cc_final: 0.8800 (p) REVERT: D 631 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 669 LEU cc_start: 0.9227 (mm) cc_final: 0.8957 (tp) REVERT: D 677 MET cc_start: 0.7934 (mmm) cc_final: 0.7726 (mmt) REVERT: D 702 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7503 (tm-30) outliers start: 4 outliers final: 0 residues processed: 609 average time/residue: 0.3048 time to fit residues: 288.5060 Evaluate side-chains 421 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 199 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 240 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 21884 Z= 0.272 Angle : 0.761 10.561 29632 Z= 0.389 Chirality : 0.042 0.190 3384 Planarity : 0.004 0.043 3724 Dihedral : 6.323 33.596 2864 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.23 % Favored : 85.62 % Rotamer: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -2.52 (0.15), residues: 2636 helix: -0.27 (0.13), residues: 1484 sheet: -4.44 (0.44), residues: 48 loop : -3.63 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 493 HIS 0.007 0.001 HIS B 256 PHE 0.017 0.002 PHE A 597 TYR 0.022 0.002 TYR D 661 ARG 0.009 0.001 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.9254 (tttt) cc_final: 0.9005 (ptpt) REVERT: A 177 LEU cc_start: 0.8607 (pp) cc_final: 0.8395 (mt) REVERT: A 321 TYR cc_start: 0.8171 (t80) cc_final: 0.7800 (t80) REVERT: A 323 MET cc_start: 0.7755 (tpt) cc_final: 0.7537 (tpt) REVERT: A 448 TYR cc_start: 0.8719 (t80) cc_final: 0.8461 (t80) REVERT: A 493 TRP cc_start: 0.6812 (m100) cc_final: 0.6290 (m100) REVERT: A 512 ASP cc_start: 0.6239 (m-30) cc_final: 0.5864 (t0) REVERT: A 574 MET cc_start: 0.7946 (ppp) cc_final: 0.7084 (ppp) REVERT: A 578 MET cc_start: 0.8300 (mtp) cc_final: 0.7918 (mtm) REVERT: A 631 GLU cc_start: 0.7865 (mp0) cc_final: 0.7664 (mp0) REVERT: B 124 PHE cc_start: 0.8178 (m-10) cc_final: 0.7880 (m-80) REVERT: B 173 MET cc_start: 0.8404 (mtt) cc_final: 0.8186 (mmm) REVERT: B 303 LEU cc_start: 0.9539 (mp) cc_final: 0.9237 (tp) REVERT: B 336 MET cc_start: 0.7988 (ttt) cc_final: 0.7663 (tpp) REVERT: B 388 SER cc_start: 0.8714 (m) cc_final: 0.8196 (p) REVERT: B 448 TYR cc_start: 0.8675 (t80) cc_final: 0.8013 (t80) REVERT: B 493 TRP cc_start: 0.7297 (m100) cc_final: 0.6330 (m100) REVERT: B 512 ASP cc_start: 0.6693 (m-30) cc_final: 0.6428 (t0) REVERT: B 550 CYS cc_start: 0.8686 (t) cc_final: 0.8473 (t) REVERT: B 572 MET cc_start: 0.9336 (mmm) cc_final: 0.9109 (mmm) REVERT: B 574 MET cc_start: 0.7685 (ppp) cc_final: 0.7070 (ppp) REVERT: B 578 MET cc_start: 0.8611 (mtp) cc_final: 0.8138 (mtm) REVERT: C 141 ASP cc_start: 0.9243 (t0) cc_final: 0.9035 (t0) REVERT: C 388 SER cc_start: 0.8630 (m) cc_final: 0.7712 (p) REVERT: C 448 TYR cc_start: 0.8897 (t80) cc_final: 0.8541 (t80) REVERT: C 455 LEU cc_start: 0.9532 (tp) cc_final: 0.9199 (tp) REVERT: C 574 MET cc_start: 0.7742 (ppp) cc_final: 0.7087 (ppp) REVERT: C 578 MET cc_start: 0.8744 (mtp) cc_final: 0.8338 (mtm) REVERT: C 632 LEU cc_start: 0.9361 (mt) cc_final: 0.9049 (mm) REVERT: C 735 ASN cc_start: 0.7452 (m110) cc_final: 0.7163 (m110) REVERT: D 321 TYR cc_start: 0.8201 (t80) cc_final: 0.7726 (t80) REVERT: D 418 GLU cc_start: 0.8586 (mp0) cc_final: 0.8386 (mp0) REVERT: D 455 LEU cc_start: 0.9339 (tp) cc_final: 0.8788 (tp) REVERT: D 493 TRP cc_start: 0.7175 (m100) cc_final: 0.6140 (m100) REVERT: D 512 ASP cc_start: 0.6195 (m-30) cc_final: 0.5847 (t0) REVERT: D 548 LEU cc_start: 0.9187 (tp) cc_final: 0.8940 (pt) REVERT: D 553 LEU cc_start: 0.9386 (tt) cc_final: 0.9171 (pp) REVERT: D 555 MET cc_start: 0.8895 (ttt) cc_final: 0.8607 (ttt) REVERT: D 574 MET cc_start: 0.8002 (ppp) cc_final: 0.7191 (ppp) REVERT: D 578 MET cc_start: 0.8572 (mtp) cc_final: 0.8210 (mtm) REVERT: D 611 LYS cc_start: 0.7680 (tmtt) cc_final: 0.7389 (ttpt) REVERT: D 631 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7521 (tm-30) REVERT: D 635 LEU cc_start: 0.9273 (mt) cc_final: 0.8933 (mt) REVERT: D 733 ARG cc_start: 0.7238 (mmm160) cc_final: 0.7025 (mmm160) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.3044 time to fit residues: 249.1191 Evaluate side-chains 376 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 20.0000 chunk 255 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 228 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21884 Z= 0.181 Angle : 0.700 10.119 29632 Z= 0.353 Chirality : 0.040 0.153 3384 Planarity : 0.004 0.048 3724 Dihedral : 5.867 31.797 2864 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.13 % Favored : 86.72 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.15 (0.16), residues: 2636 helix: 0.14 (0.13), residues: 1460 sheet: -4.24 (0.51), residues: 48 loop : -3.59 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 493 HIS 0.004 0.001 HIS C 417 PHE 0.025 0.001 PHE D 590 TYR 0.015 0.001 TYR A 409 ARG 0.005 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 542 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.9273 (tp) cc_final: 0.9063 (tp) REVERT: A 321 TYR cc_start: 0.7923 (t80) cc_final: 0.7559 (t80) REVERT: A 448 TYR cc_start: 0.8909 (t80) cc_final: 0.8628 (t80) REVERT: A 451 TYR cc_start: 0.8578 (t80) cc_final: 0.8360 (t80) REVERT: A 455 LEU cc_start: 0.9147 (tp) cc_final: 0.8827 (tp) REVERT: A 493 TRP cc_start: 0.6721 (m100) cc_final: 0.6352 (m100) REVERT: A 512 ASP cc_start: 0.6181 (m-30) cc_final: 0.5782 (t0) REVERT: A 529 GLN cc_start: 0.9290 (tp40) cc_final: 0.8870 (mm110) REVERT: A 550 CYS cc_start: 0.8770 (t) cc_final: 0.8507 (t) REVERT: A 574 MET cc_start: 0.7893 (ppp) cc_final: 0.7064 (ppp) REVERT: A 578 MET cc_start: 0.8419 (mtp) cc_final: 0.8148 (mtm) REVERT: A 668 LEU cc_start: 0.9293 (mm) cc_final: 0.9072 (mm) REVERT: B 124 PHE cc_start: 0.8089 (m-10) cc_final: 0.7803 (m-80) REVERT: B 141 ASP cc_start: 0.9039 (m-30) cc_final: 0.8732 (t0) REVERT: B 323 MET cc_start: 0.7712 (tpt) cc_final: 0.7365 (tpt) REVERT: B 388 SER cc_start: 0.8649 (m) cc_final: 0.8075 (p) REVERT: B 448 TYR cc_start: 0.8945 (t80) cc_final: 0.8155 (t80) REVERT: B 493 TRP cc_start: 0.7312 (m100) cc_final: 0.6493 (m100) REVERT: B 512 ASP cc_start: 0.6678 (m-30) cc_final: 0.6324 (t0) REVERT: B 572 MET cc_start: 0.9313 (mmm) cc_final: 0.9027 (mmm) REVERT: B 574 MET cc_start: 0.7695 (ppp) cc_final: 0.7090 (ppp) REVERT: B 578 MET cc_start: 0.8759 (mtp) cc_final: 0.8480 (mtm) REVERT: B 677 MET cc_start: 0.7795 (mmm) cc_final: 0.7496 (mmt) REVERT: C 141 ASP cc_start: 0.9132 (t0) cc_final: 0.8904 (t0) REVERT: C 173 MET cc_start: 0.8231 (mmp) cc_final: 0.7980 (mmm) REVERT: C 448 TYR cc_start: 0.9078 (t80) cc_final: 0.8620 (t80) REVERT: C 455 LEU cc_start: 0.9553 (tp) cc_final: 0.9235 (tp) REVERT: C 464 ARG cc_start: 0.6266 (mtt-85) cc_final: 0.5561 (tpt-90) REVERT: C 550 CYS cc_start: 0.8839 (t) cc_final: 0.8637 (t) REVERT: C 574 MET cc_start: 0.7776 (ppp) cc_final: 0.7129 (ppp) REVERT: C 578 MET cc_start: 0.8699 (mtp) cc_final: 0.8340 (mtm) REVERT: C 632 LEU cc_start: 0.9292 (mt) cc_final: 0.9069 (mm) REVERT: D 318 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8471 (tppt) REVERT: D 418 GLU cc_start: 0.8554 (mp0) cc_final: 0.8326 (mp0) REVERT: D 448 TYR cc_start: 0.9084 (t80) cc_final: 0.8755 (t80) REVERT: D 455 LEU cc_start: 0.9281 (tp) cc_final: 0.8759 (tp) REVERT: D 493 TRP cc_start: 0.7115 (m100) cc_final: 0.6634 (m100) REVERT: D 512 ASP cc_start: 0.6088 (m-30) cc_final: 0.5837 (t0) REVERT: D 529 GLN cc_start: 0.9056 (tp40) cc_final: 0.8818 (tp40) REVERT: D 553 LEU cc_start: 0.9385 (tt) cc_final: 0.9184 (pp) REVERT: D 574 MET cc_start: 0.7989 (ppp) cc_final: 0.6882 (ppp) REVERT: D 578 MET cc_start: 0.8601 (mtp) cc_final: 0.7732 (mtp) REVERT: D 631 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7635 (tm-30) REVERT: D 632 LEU cc_start: 0.9371 (mm) cc_final: 0.9150 (mt) REVERT: D 635 LEU cc_start: 0.9185 (mt) cc_final: 0.8883 (mt) REVERT: D 669 LEU cc_start: 0.9211 (mm) cc_final: 0.8996 (tp) REVERT: D 733 ARG cc_start: 0.7179 (mmm160) cc_final: 0.6964 (mmm160) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.2967 time to fit residues: 252.7220 Evaluate side-chains 404 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 182 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 585 HIS ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 21884 Z= 0.291 Angle : 0.763 10.167 29632 Z= 0.390 Chirality : 0.042 0.157 3384 Planarity : 0.004 0.056 3724 Dihedral : 6.090 34.107 2864 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 16.12 % Favored : 83.73 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.12 (0.16), residues: 2636 helix: 0.09 (0.13), residues: 1468 sheet: -3.78 (0.60), residues: 48 loop : -3.48 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 521 HIS 0.009 0.001 HIS B 256 PHE 0.023 0.002 PHE B 597 TYR 0.025 0.002 TYR B 208 ARG 0.007 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.9527 (mt) cc_final: 0.9306 (tp) REVERT: A 493 TRP cc_start: 0.6811 (m100) cc_final: 0.6560 (m100) REVERT: A 512 ASP cc_start: 0.6400 (m-30) cc_final: 0.5927 (t0) REVERT: A 529 GLN cc_start: 0.9470 (tp40) cc_final: 0.8916 (mm110) REVERT: A 548 LEU cc_start: 0.9188 (pt) cc_final: 0.8973 (mm) REVERT: A 550 CYS cc_start: 0.8844 (t) cc_final: 0.8551 (t) REVERT: A 572 MET cc_start: 0.9039 (mmm) cc_final: 0.8757 (mmm) REVERT: A 574 MET cc_start: 0.7856 (ppp) cc_final: 0.7191 (ppp) REVERT: A 578 MET cc_start: 0.8509 (mtp) cc_final: 0.8265 (mtm) REVERT: B 141 ASP cc_start: 0.9055 (m-30) cc_final: 0.8761 (t0) REVERT: B 318 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8598 (tppp) REVERT: B 388 SER cc_start: 0.8860 (m) cc_final: 0.8295 (p) REVERT: B 448 TYR cc_start: 0.9063 (t80) cc_final: 0.8834 (t80) REVERT: B 493 TRP cc_start: 0.7546 (m100) cc_final: 0.6692 (m100) REVERT: B 574 MET cc_start: 0.7738 (ppp) cc_final: 0.6932 (ppp) REVERT: B 578 MET cc_start: 0.8718 (mtp) cc_final: 0.8037 (mtm) REVERT: B 630 LEU cc_start: 0.8459 (mm) cc_final: 0.8081 (mm) REVERT: B 632 LEU cc_start: 0.9409 (mt) cc_final: 0.9199 (mt) REVERT: C 141 ASP cc_start: 0.9155 (t0) cc_final: 0.8914 (t0) REVERT: C 404 LEU cc_start: 0.9189 (tt) cc_final: 0.8960 (tt) REVERT: C 418 GLU cc_start: 0.9199 (mp0) cc_final: 0.8681 (mp0) REVERT: C 448 TYR cc_start: 0.9130 (t80) cc_final: 0.8803 (t80) REVERT: C 455 LEU cc_start: 0.9507 (tp) cc_final: 0.9202 (tp) REVERT: C 464 ARG cc_start: 0.6227 (mtt-85) cc_final: 0.5656 (tpt-90) REVERT: C 574 MET cc_start: 0.7839 (ppp) cc_final: 0.7018 (ppp) REVERT: C 578 MET cc_start: 0.8778 (mtp) cc_final: 0.8387 (mtm) REVERT: C 632 LEU cc_start: 0.9379 (mt) cc_final: 0.9099 (mm) REVERT: D 418 GLU cc_start: 0.8819 (mp0) cc_final: 0.8320 (mp0) REVERT: D 451 TYR cc_start: 0.8526 (t80) cc_final: 0.8292 (t80) REVERT: D 512 ASP cc_start: 0.6367 (m-30) cc_final: 0.5859 (t0) REVERT: D 529 GLN cc_start: 0.9533 (tp40) cc_final: 0.8841 (tp40) REVERT: D 548 LEU cc_start: 0.9306 (pt) cc_final: 0.9055 (mm) REVERT: D 557 LEU cc_start: 0.9229 (tp) cc_final: 0.8859 (tp) REVERT: D 572 MET cc_start: 0.8997 (mmm) cc_final: 0.8794 (mmm) REVERT: D 578 MET cc_start: 0.8617 (mtp) cc_final: 0.8086 (mtt) REVERT: D 635 LEU cc_start: 0.9269 (mt) cc_final: 0.8904 (mt) REVERT: D 730 LEU cc_start: 0.9220 (pt) cc_final: 0.8993 (pt) REVERT: D 733 ARG cc_start: 0.7144 (mmm160) cc_final: 0.6925 (mmm160) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.2935 time to fit residues: 229.6068 Evaluate side-chains 374 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 84 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 477 HIS B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 21884 Z= 0.290 Angle : 0.767 9.876 29632 Z= 0.392 Chirality : 0.042 0.165 3384 Planarity : 0.005 0.126 3724 Dihedral : 6.066 33.879 2864 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.25 % Favored : 84.60 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.13 (0.16), residues: 2636 helix: 0.07 (0.13), residues: 1468 sheet: -3.48 (0.65), residues: 48 loop : -3.48 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 742 HIS 0.007 0.001 HIS B 256 PHE 0.022 0.002 PHE B 597 TYR 0.029 0.002 TYR B 547 ARG 0.013 0.001 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.9542 (mt) cc_final: 0.9270 (tp) REVERT: A 318 LYS cc_start: 0.8869 (tppt) cc_final: 0.8582 (tppp) REVERT: A 455 LEU cc_start: 0.9167 (tp) cc_final: 0.8955 (tp) REVERT: A 493 TRP cc_start: 0.6960 (m100) cc_final: 0.6341 (m100) REVERT: A 512 ASP cc_start: 0.6499 (m-30) cc_final: 0.5869 (t0) REVERT: A 529 GLN cc_start: 0.9558 (tp40) cc_final: 0.8851 (mm110) REVERT: A 548 LEU cc_start: 0.9307 (pt) cc_final: 0.9057 (mt) REVERT: A 550 CYS cc_start: 0.8997 (t) cc_final: 0.8672 (t) REVERT: A 557 LEU cc_start: 0.9253 (tp) cc_final: 0.9030 (tp) REVERT: A 572 MET cc_start: 0.8955 (mmm) cc_final: 0.8632 (mmm) REVERT: A 574 MET cc_start: 0.7879 (ppp) cc_final: 0.7160 (ppp) REVERT: A 578 MET cc_start: 0.8541 (mtp) cc_final: 0.8061 (mtm) REVERT: A 630 LEU cc_start: 0.8381 (mm) cc_final: 0.8168 (mm) REVERT: A 691 ILE cc_start: 0.9480 (mp) cc_final: 0.9019 (mm) REVERT: B 141 ASP cc_start: 0.9052 (m-30) cc_final: 0.8745 (t0) REVERT: B 318 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8487 (tppp) REVERT: B 388 SER cc_start: 0.8748 (m) cc_final: 0.8241 (p) REVERT: B 448 TYR cc_start: 0.9146 (t80) cc_final: 0.8824 (t80) REVERT: B 484 LEU cc_start: 0.8752 (tp) cc_final: 0.8488 (pp) REVERT: B 557 LEU cc_start: 0.8951 (tt) cc_final: 0.8748 (tt) REVERT: B 574 MET cc_start: 0.7878 (ppp) cc_final: 0.7048 (ppp) REVERT: B 578 MET cc_start: 0.8737 (mtp) cc_final: 0.8004 (mtm) REVERT: B 630 LEU cc_start: 0.8449 (mm) cc_final: 0.8138 (mm) REVERT: C 141 ASP cc_start: 0.9148 (t0) cc_final: 0.8901 (t0) REVERT: C 418 GLU cc_start: 0.9098 (mp0) cc_final: 0.8746 (mp0) REVERT: C 448 TYR cc_start: 0.9134 (t80) cc_final: 0.8716 (t80) REVERT: C 455 LEU cc_start: 0.9496 (tp) cc_final: 0.8872 (tp) REVERT: C 529 GLN cc_start: 0.9201 (tp40) cc_final: 0.8821 (mm110) REVERT: C 550 CYS cc_start: 0.8821 (t) cc_final: 0.8617 (t) REVERT: C 574 MET cc_start: 0.7899 (ppp) cc_final: 0.7122 (ppp) REVERT: C 578 MET cc_start: 0.8781 (mtp) cc_final: 0.8437 (mtm) REVERT: C 632 LEU cc_start: 0.9394 (mt) cc_final: 0.9155 (mm) REVERT: C 672 MET cc_start: 0.7979 (tpt) cc_final: 0.7637 (tpt) REVERT: D 318 LYS cc_start: 0.8817 (tppt) cc_final: 0.8560 (tppp) REVERT: D 373 LEU cc_start: 0.9351 (mt) cc_final: 0.8681 (mt) REVERT: D 493 TRP cc_start: 0.7876 (m100) cc_final: 0.7450 (m100) REVERT: D 512 ASP cc_start: 0.6441 (m-30) cc_final: 0.5967 (t0) REVERT: D 529 GLN cc_start: 0.9519 (tp40) cc_final: 0.8793 (tp40) REVERT: D 548 LEU cc_start: 0.9275 (pt) cc_final: 0.8951 (mm) REVERT: D 557 LEU cc_start: 0.9270 (tp) cc_final: 0.8939 (tp) REVERT: D 572 MET cc_start: 0.8924 (mmm) cc_final: 0.8626 (mmm) REVERT: D 574 MET cc_start: 0.7937 (ppp) cc_final: 0.6560 (ppp) REVERT: D 578 MET cc_start: 0.8527 (mtp) cc_final: 0.7398 (mtp) REVERT: D 730 LEU cc_start: 0.9200 (pt) cc_final: 0.8994 (pt) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.3037 time to fit residues: 228.3533 Evaluate side-chains 365 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.3980 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 142 optimal weight: 0.0070 chunk 254 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 114 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21884 Z= 0.244 Angle : 0.754 9.487 29632 Z= 0.380 Chirality : 0.041 0.171 3384 Planarity : 0.004 0.062 3724 Dihedral : 5.944 33.776 2864 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.40 % Favored : 84.45 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.05 (0.16), residues: 2636 helix: 0.10 (0.13), residues: 1468 sheet: -3.44 (0.66), residues: 48 loop : -3.41 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 742 HIS 0.006 0.001 HIS B 256 PHE 0.022 0.001 PHE B 597 TYR 0.022 0.002 TYR B 594 ARG 0.005 0.000 ARG A 714 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.9239 (tp) cc_final: 0.9027 (tp) REVERT: A 318 LYS cc_start: 0.8849 (tppt) cc_final: 0.8577 (tppp) REVERT: A 493 TRP cc_start: 0.7042 (m100) cc_final: 0.6560 (m100) REVERT: A 512 ASP cc_start: 0.6498 (m-30) cc_final: 0.5850 (t0) REVERT: A 529 GLN cc_start: 0.9508 (tp40) cc_final: 0.8999 (tp40) REVERT: A 548 LEU cc_start: 0.9332 (pt) cc_final: 0.9090 (mt) REVERT: A 557 LEU cc_start: 0.9200 (tp) cc_final: 0.8974 (tp) REVERT: A 572 MET cc_start: 0.8778 (mmm) cc_final: 0.8498 (mmm) REVERT: A 574 MET cc_start: 0.7739 (ppp) cc_final: 0.7028 (ppp) REVERT: A 578 MET cc_start: 0.8529 (mtp) cc_final: 0.8064 (mtm) REVERT: B 141 ASP cc_start: 0.9027 (m-30) cc_final: 0.8711 (t0) REVERT: B 318 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8572 (tppp) REVERT: B 388 SER cc_start: 0.8955 (m) cc_final: 0.8422 (p) REVERT: B 401 ASN cc_start: 0.8046 (t0) cc_final: 0.7782 (t0) REVERT: B 448 TYR cc_start: 0.9172 (t80) cc_final: 0.8657 (t80) REVERT: B 464 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7301 (mtp-110) REVERT: B 484 LEU cc_start: 0.8702 (tp) cc_final: 0.8421 (pp) REVERT: B 493 TRP cc_start: 0.7537 (m100) cc_final: 0.6430 (m100) REVERT: B 574 MET cc_start: 0.7801 (ppp) cc_final: 0.6690 (ppp) REVERT: B 578 MET cc_start: 0.8688 (mtp) cc_final: 0.7974 (mtt) REVERT: B 632 LEU cc_start: 0.9361 (mt) cc_final: 0.9099 (mt) REVERT: C 141 ASP cc_start: 0.9143 (t0) cc_final: 0.8887 (t0) REVERT: C 418 GLU cc_start: 0.9025 (mp0) cc_final: 0.8728 (mp0) REVERT: C 451 TYR cc_start: 0.8746 (t80) cc_final: 0.8525 (t80) REVERT: C 453 ILE cc_start: 0.9208 (mm) cc_final: 0.8938 (tp) REVERT: C 464 ARG cc_start: 0.6053 (mtt-85) cc_final: 0.5523 (ttt180) REVERT: C 529 GLN cc_start: 0.9394 (tp40) cc_final: 0.8920 (tp40) REVERT: C 550 CYS cc_start: 0.8486 (t) cc_final: 0.8270 (t) REVERT: C 574 MET cc_start: 0.7712 (ppp) cc_final: 0.7029 (ppp) REVERT: C 578 MET cc_start: 0.8759 (mtp) cc_final: 0.8408 (mtm) REVERT: C 632 LEU cc_start: 0.9376 (mt) cc_final: 0.9125 (mm) REVERT: C 672 MET cc_start: 0.7961 (tpt) cc_final: 0.7634 (tpt) REVERT: D 268 LEU cc_start: 0.9271 (tp) cc_final: 0.9010 (tp) REVERT: D 318 LYS cc_start: 0.8853 (tppt) cc_final: 0.8559 (tppp) REVERT: D 373 LEU cc_start: 0.9332 (mt) cc_final: 0.8653 (mt) REVERT: D 512 ASP cc_start: 0.6502 (m-30) cc_final: 0.5958 (t0) REVERT: D 529 GLN cc_start: 0.9499 (tp40) cc_final: 0.8775 (tp40) REVERT: D 555 MET cc_start: 0.8917 (tpp) cc_final: 0.8504 (tpp) REVERT: D 557 LEU cc_start: 0.9280 (tp) cc_final: 0.8882 (tp) REVERT: D 578 MET cc_start: 0.8544 (mtp) cc_final: 0.8066 (mtt) REVERT: D 730 LEU cc_start: 0.9176 (pt) cc_final: 0.8967 (pt) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.2885 time to fit residues: 223.8891 Evaluate side-chains 370 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21884 Z= 0.189 Angle : 0.742 9.733 29632 Z= 0.365 Chirality : 0.040 0.165 3384 Planarity : 0.004 0.063 3724 Dihedral : 5.673 32.375 2864 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.04 % Favored : 85.81 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.88 (0.17), residues: 2636 helix: 0.22 (0.13), residues: 1468 sheet: -3.56 (0.64), residues: 48 loop : -3.28 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 742 HIS 0.003 0.000 HIS B 417 PHE 0.025 0.001 PHE B 597 TYR 0.026 0.001 TYR B 547 ARG 0.004 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 TRP cc_start: 0.6928 (m100) cc_final: 0.6450 (m100) REVERT: A 512 ASP cc_start: 0.6383 (m-30) cc_final: 0.5804 (t0) REVERT: A 529 GLN cc_start: 0.9460 (tp40) cc_final: 0.9047 (tp40) REVERT: A 548 LEU cc_start: 0.9276 (pt) cc_final: 0.9014 (mt) REVERT: A 572 MET cc_start: 0.8730 (mmm) cc_final: 0.8436 (mmm) REVERT: A 574 MET cc_start: 0.7673 (ppp) cc_final: 0.6963 (ppp) REVERT: A 578 MET cc_start: 0.8644 (mtp) cc_final: 0.8216 (mtm) REVERT: A 730 LEU cc_start: 0.9259 (pt) cc_final: 0.9049 (pt) REVERT: B 141 ASP cc_start: 0.9024 (m-30) cc_final: 0.8690 (t70) REVERT: B 388 SER cc_start: 0.8840 (m) cc_final: 0.8341 (p) REVERT: B 401 ASN cc_start: 0.8044 (t0) cc_final: 0.7742 (t0) REVERT: B 448 TYR cc_start: 0.9131 (t80) cc_final: 0.8614 (t80) REVERT: B 464 ARG cc_start: 0.7583 (mtp180) cc_final: 0.7132 (mtp-110) REVERT: B 484 LEU cc_start: 0.8651 (tp) cc_final: 0.8340 (pp) REVERT: B 493 TRP cc_start: 0.7425 (m100) cc_final: 0.6229 (m100) REVERT: B 574 MET cc_start: 0.7772 (ppp) cc_final: 0.6802 (ppp) REVERT: B 578 MET cc_start: 0.8713 (mtp) cc_final: 0.8106 (mtm) REVERT: C 141 ASP cc_start: 0.9144 (t0) cc_final: 0.8871 (t0) REVERT: C 418 GLU cc_start: 0.9053 (mp0) cc_final: 0.8798 (mp0) REVERT: C 448 TYR cc_start: 0.9181 (t80) cc_final: 0.8784 (t80) REVERT: C 451 TYR cc_start: 0.8671 (t80) cc_final: 0.8439 (t80) REVERT: C 453 ILE cc_start: 0.9162 (mm) cc_final: 0.8910 (tp) REVERT: C 455 LEU cc_start: 0.9353 (tp) cc_final: 0.8770 (tp) REVERT: C 464 ARG cc_start: 0.6254 (mtt-85) cc_final: 0.5624 (ttt180) REVERT: C 529 GLN cc_start: 0.9379 (tp40) cc_final: 0.8842 (tp40) REVERT: C 555 MET cc_start: 0.8505 (mtp) cc_final: 0.8208 (tpt) REVERT: C 574 MET cc_start: 0.7720 (ppp) cc_final: 0.7037 (ppp) REVERT: C 578 MET cc_start: 0.8771 (mtp) cc_final: 0.8476 (mtm) REVERT: C 632 LEU cc_start: 0.9300 (mt) cc_final: 0.8994 (mt) REVERT: C 672 MET cc_start: 0.7932 (tpt) cc_final: 0.7629 (tpt) REVERT: C 733 ARG cc_start: 0.7187 (mmm160) cc_final: 0.6553 (mmm160) REVERT: D 493 TRP cc_start: 0.7713 (m100) cc_final: 0.7261 (m100) REVERT: D 512 ASP cc_start: 0.6458 (m-30) cc_final: 0.5969 (t0) REVERT: D 529 GLN cc_start: 0.9380 (tp40) cc_final: 0.8654 (tp40) REVERT: D 548 LEU cc_start: 0.9200 (pt) cc_final: 0.8927 (mt) REVERT: D 557 LEU cc_start: 0.9257 (tp) cc_final: 0.8868 (tp) REVERT: D 578 MET cc_start: 0.8587 (mtp) cc_final: 0.7927 (mtt) REVERT: D 614 LYS cc_start: 0.6513 (mmpt) cc_final: 0.6313 (mmpt) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.2845 time to fit residues: 221.8764 Evaluate side-chains 385 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 214 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 30.0000 chunk 155 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 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21884 Z= 0.220 Angle : 0.746 9.919 29632 Z= 0.370 Chirality : 0.041 0.173 3384 Planarity : 0.004 0.064 3724 Dihedral : 5.687 35.253 2864 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.21 % Favored : 84.64 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.88 (0.17), residues: 2636 helix: 0.25 (0.13), residues: 1464 sheet: -3.48 (0.65), residues: 48 loop : -3.33 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 742 HIS 0.003 0.001 HIS C 256 PHE 0.030 0.001 PHE B 590 TYR 0.018 0.001 TYR B 594 ARG 0.005 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ILE cc_start: 0.8981 (mm) cc_final: 0.8777 (tp) REVERT: A 493 TRP cc_start: 0.6977 (m100) cc_final: 0.6447 (m100) REVERT: A 529 GLN cc_start: 0.9506 (tp40) cc_final: 0.9016 (tp40) REVERT: A 548 LEU cc_start: 0.9267 (pt) cc_final: 0.9041 (mt) REVERT: A 557 LEU cc_start: 0.9229 (tp) cc_final: 0.8946 (tp) REVERT: A 572 MET cc_start: 0.8757 (mmm) cc_final: 0.8457 (mmm) REVERT: A 574 MET cc_start: 0.7618 (ppp) cc_final: 0.6900 (ppp) REVERT: A 578 MET cc_start: 0.8537 (mtp) cc_final: 0.7955 (mtm) REVERT: A 730 LEU cc_start: 0.9251 (pt) cc_final: 0.9041 (pt) REVERT: B 141 ASP cc_start: 0.9018 (m-30) cc_final: 0.8681 (t70) REVERT: B 388 SER cc_start: 0.8925 (m) cc_final: 0.8410 (p) REVERT: B 401 ASN cc_start: 0.8036 (t0) cc_final: 0.7824 (t0) REVERT: B 440 MET cc_start: 0.8402 (mmp) cc_final: 0.8193 (mmp) REVERT: B 464 ARG cc_start: 0.7650 (mtp180) cc_final: 0.7320 (mtp-110) REVERT: B 484 LEU cc_start: 0.8637 (tp) cc_final: 0.8338 (pp) REVERT: B 493 TRP cc_start: 0.7097 (m100) cc_final: 0.6793 (m100) REVERT: B 574 MET cc_start: 0.7827 (ppp) cc_final: 0.6321 (ppp) REVERT: B 578 MET cc_start: 0.8668 (mtp) cc_final: 0.7493 (mtp) REVERT: C 141 ASP cc_start: 0.9140 (t0) cc_final: 0.8860 (t0) REVERT: C 418 GLU cc_start: 0.9021 (mp0) cc_final: 0.8738 (mp0) REVERT: C 453 ILE cc_start: 0.9171 (mm) cc_final: 0.8886 (tp) REVERT: C 493 TRP cc_start: 0.7782 (m100) cc_final: 0.6461 (m100) REVERT: C 574 MET cc_start: 0.7692 (ppp) cc_final: 0.6846 (ppp) REVERT: C 578 MET cc_start: 0.8811 (mtp) cc_final: 0.8482 (mtm) REVERT: C 632 LEU cc_start: 0.9371 (mt) cc_final: 0.9037 (mt) REVERT: C 672 MET cc_start: 0.7999 (tpt) cc_final: 0.7666 (tpt) REVERT: C 730 LEU cc_start: 0.9169 (pt) cc_final: 0.8967 (pt) REVERT: D 493 TRP cc_start: 0.7642 (m100) cc_final: 0.7266 (m100) REVERT: D 512 ASP cc_start: 0.6466 (m-30) cc_final: 0.5830 (t0) REVERT: D 529 GLN cc_start: 0.9406 (tp40) cc_final: 0.8560 (tp40) REVERT: D 548 LEU cc_start: 0.9192 (pt) cc_final: 0.8960 (mt) REVERT: D 555 MET cc_start: 0.8942 (tpp) cc_final: 0.8704 (tpp) REVERT: D 557 LEU cc_start: 0.9255 (tp) cc_final: 0.8806 (tp) REVERT: D 572 MET cc_start: 0.8872 (mmm) cc_final: 0.8637 (mmm) REVERT: D 574 MET cc_start: 0.7788 (ppp) cc_final: 0.6909 (ppp) REVERT: D 578 MET cc_start: 0.8585 (mtp) cc_final: 0.8205 (mtm) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.2767 time to fit residues: 206.2030 Evaluate side-chains 363 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 263 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 585 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 21884 Z= 0.286 Angle : 0.794 11.049 29632 Z= 0.399 Chirality : 0.043 0.211 3384 Planarity : 0.004 0.066 3724 Dihedral : 5.915 35.969 2864 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.59 % Favored : 84.26 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.99 (0.17), residues: 2636 helix: 0.15 (0.13), residues: 1464 sheet: -3.43 (0.66), residues: 48 loop : -3.37 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 521 HIS 0.004 0.001 HIS B 256 PHE 0.029 0.002 PHE B 590 TYR 0.022 0.002 TYR B 547 ARG 0.005 0.001 ARG A 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 TRP cc_start: 0.7151 (m100) cc_final: 0.6433 (m100) REVERT: A 529 GLN cc_start: 0.9554 (tp40) cc_final: 0.8854 (tp40) REVERT: A 548 LEU cc_start: 0.9326 (pt) cc_final: 0.9052 (mm) REVERT: A 557 LEU cc_start: 0.9333 (tp) cc_final: 0.9015 (tp) REVERT: A 572 MET cc_start: 0.8772 (mmm) cc_final: 0.8495 (mmm) REVERT: A 574 MET cc_start: 0.7723 (ppp) cc_final: 0.6969 (ppp) REVERT: A 578 MET cc_start: 0.8541 (mtp) cc_final: 0.8065 (mtm) REVERT: A 730 LEU cc_start: 0.9258 (pt) cc_final: 0.9045 (pt) REVERT: B 141 ASP cc_start: 0.9082 (m-30) cc_final: 0.8720 (t0) REVERT: B 388 SER cc_start: 0.9082 (m) cc_final: 0.8476 (p) REVERT: B 464 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7408 (mtp-110) REVERT: B 484 LEU cc_start: 0.8555 (tp) cc_final: 0.8268 (pp) REVERT: B 493 TRP cc_start: 0.7331 (m100) cc_final: 0.6887 (m100) REVERT: B 578 MET cc_start: 0.8651 (mtp) cc_final: 0.8256 (mtm) REVERT: C 134 GLU cc_start: 0.8349 (pm20) cc_final: 0.8104 (pm20) REVERT: C 141 ASP cc_start: 0.9138 (t0) cc_final: 0.8864 (t0) REVERT: C 418 GLU cc_start: 0.9050 (mp0) cc_final: 0.8763 (mp0) REVERT: C 453 ILE cc_start: 0.9187 (mm) cc_final: 0.8954 (tp) REVERT: C 574 MET cc_start: 0.7812 (ppp) cc_final: 0.7033 (ppp) REVERT: C 578 MET cc_start: 0.8795 (mtp) cc_final: 0.8270 (mtm) REVERT: C 597 PHE cc_start: 0.8522 (m-80) cc_final: 0.8236 (m-10) REVERT: C 632 LEU cc_start: 0.9439 (mt) cc_final: 0.9121 (mm) REVERT: C 672 MET cc_start: 0.8057 (tpt) cc_final: 0.7710 (tpt) REVERT: D 373 LEU cc_start: 0.9308 (mt) cc_final: 0.8795 (mt) REVERT: D 451 TYR cc_start: 0.8503 (t80) cc_final: 0.8291 (t80) REVERT: D 529 GLN cc_start: 0.9499 (tp40) cc_final: 0.8548 (tp40) REVERT: D 548 LEU cc_start: 0.9251 (pt) cc_final: 0.8977 (mt) REVERT: D 557 LEU cc_start: 0.9181 (tp) cc_final: 0.8671 (tp) REVERT: D 572 MET cc_start: 0.8893 (mmm) cc_final: 0.8629 (mmm) REVERT: D 574 MET cc_start: 0.7883 (ppp) cc_final: 0.7015 (ppp) REVERT: D 578 MET cc_start: 0.8578 (mtp) cc_final: 0.8076 (mtm) REVERT: D 672 MET cc_start: 0.8572 (tpt) cc_final: 0.8350 (tpt) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.2974 time to fit residues: 219.7504 Evaluate side-chains 360 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 209 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 215 optimal weight: 0.0170 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.064233 restraints weight = 86595.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065714 restraints weight = 61402.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066690 restraints weight = 47185.537| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.6398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21884 Z= 0.209 Angle : 0.759 10.683 29632 Z= 0.375 Chirality : 0.041 0.169 3384 Planarity : 0.004 0.041 3724 Dihedral : 5.688 35.562 2864 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.72 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.88 (0.17), residues: 2636 helix: 0.24 (0.13), residues: 1460 sheet: -3.42 (0.66), residues: 48 loop : -3.30 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 742 HIS 0.003 0.001 HIS C 256 PHE 0.026 0.001 PHE D 590 TYR 0.015 0.001 TYR D 661 ARG 0.004 0.000 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4685.31 seconds wall clock time: 85 minutes 40.43 seconds (5140.43 seconds total)