Starting phenix.real_space_refine on Sun Sep 29 03:48:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/09_2024/6pvp_20496.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/09_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_20496/09_2024/6pvp_20496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/09_2024/6pvp_20496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/09_2024/6pvp_20496.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvp_20496/09_2024/6pvp_20496.cif" } 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. Time to flip 56 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21425 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 12.84, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 3.0 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: 2.03 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: 5.70 Time building geometry restraints manager: 6.44 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: 0.00 - 2.38: 28031 2.38 - 4.76: 1265 4.76 - 7.14: 255 7.14 - 9.52: 57 9.52 - 11.90: 24 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 3.040 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR C 594 " pdb=" OG1 THR C 636 " model vdw 2.282 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 45.820 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.330 ------------------------------------------------------------------------------- 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 : 2.509 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: 0.3340 time to fit residues: 356.7673 Evaluate side-chains 421 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 418 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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: 6.9990 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** 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 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** 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** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21884 Z= 0.258 Angle : 0.811 9.454 29632 Z= 0.427 Chirality : 0.043 0.169 3384 Planarity : 0.005 0.042 3724 Dihedral : 6.710 37.235 2864 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.69 % Favored : 86.00 % Rotamer: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -3.24 (0.15), residues: 2636 helix: -1.04 (0.12), residues: 1456 sheet: -5.30 (0.32), residues: 64 loop : -3.51 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 739 HIS 0.006 0.001 HIS B 256 PHE 0.024 0.002 PHE A 124 TYR 0.016 0.002 TYR B 359 ARG 0.007 0.001 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 587 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 583 time to evaluate : 2.572 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: A 134 GLU cc_start: 0.8623 (pm20) cc_final: 0.8355 (pm20) REVERT: A 156 ASP cc_start: 0.9044 (m-30) cc_final: 0.8819 (m-30) REVERT: A 173 MET cc_start: 0.8371 (mtm) cc_final: 0.7987 (mmm) REVERT: A 321 TYR cc_start: 0.8343 (t80) cc_final: 0.8020 (t80) REVERT: A 388 SER cc_start: 0.8149 (m) cc_final: 0.7927 (p) REVERT: A 448 TYR cc_start: 0.8472 (t80) cc_final: 0.8004 (t80) REVERT: A 464 ARG cc_start: 0.7168 (ttt180) cc_final: 0.6726 (ttt180) REVERT: A 493 TRP cc_start: 0.6971 (m100) cc_final: 0.6688 (m100) REVERT: A 512 ASP cc_start: 0.6193 (m-30) cc_final: 0.5771 (t0) REVERT: A 550 CYS cc_start: 0.8913 (t) cc_final: 0.8688 (t) REVERT: A 557 LEU cc_start: 0.9074 (tt) cc_final: 0.8854 (mm) REVERT: A 574 MET cc_start: 0.8048 (ppp) cc_final: 0.7445 (ppp) REVERT: A 578 MET cc_start: 0.8399 (mtp) cc_final: 0.7950 (mtm) REVERT: A 702 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 134 GLU cc_start: 0.8650 (pm20) cc_final: 0.8445 (pm20) REVERT: B 234 LEU cc_start: 0.9245 (mm) cc_final: 0.9008 (mm) REVERT: B 271 CYS cc_start: 0.9416 (m) cc_final: 0.8665 (t) REVERT: B 448 TYR cc_start: 0.8579 (t80) cc_final: 0.7500 (t80) REVERT: B 464 ARG cc_start: 0.6947 (ttt180) cc_final: 0.6478 (ttt180) REVERT: B 484 LEU cc_start: 0.8595 (tp) cc_final: 0.8359 (tp) REVERT: B 493 TRP cc_start: 0.7174 (m100) cc_final: 0.6259 (m100) REVERT: B 512 ASP cc_start: 0.6746 (m-30) cc_final: 0.6402 (t0) REVERT: B 555 MET cc_start: 0.8679 (ttt) cc_final: 0.8376 (ttt) REVERT: B 574 MET cc_start: 0.7630 (ppp) cc_final: 0.6900 (ppp) REVERT: B 578 MET cc_start: 0.8622 (mtp) cc_final: 0.8315 (mtm) REVERT: B 632 LEU cc_start: 0.9335 (mt) cc_final: 0.9124 (mt) REVERT: B 687 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 735 ASN cc_start: 0.6609 (m110) cc_final: 0.6309 (m110) REVERT: C 158 LEU cc_start: 0.9347 (tt) cc_final: 0.9146 (pp) REVERT: C 173 MET cc_start: 0.8370 (mmp) cc_final: 0.7667 (mmp) REVERT: C 388 SER cc_start: 0.8443 (m) cc_final: 0.7785 (p) REVERT: C 448 TYR cc_start: 0.8717 (t80) cc_final: 0.8298 (t80) REVERT: C 455 LEU cc_start: 0.9523 (tp) cc_final: 0.9224 (tp) REVERT: C 529 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8852 (tm-30) REVERT: C 574 MET cc_start: 0.7797 (ppp) cc_final: 0.6946 (ppp) REVERT: C 578 MET cc_start: 0.8641 (mtp) cc_final: 0.8181 (mtm) REVERT: C 632 LEU cc_start: 0.9269 (mt) cc_final: 0.8941 (mm) REVERT: C 735 ASN cc_start: 0.7761 (m110) cc_final: 0.7492 (m110) REVERT: D 120 LYS cc_start: 0.9272 (tttt) cc_final: 0.9047 (ptpt) REVERT: D 134 GLU cc_start: 0.8585 (pm20) cc_final: 0.8254 (pm20) REVERT: D 156 ASP cc_start: 0.9000 (m-30) cc_final: 0.8772 (m-30) REVERT: D 173 MET cc_start: 0.8394 (mtm) cc_final: 0.8081 (mmm) REVERT: D 321 TYR cc_start: 0.8376 (t80) cc_final: 0.8134 (t80) REVERT: D 418 GLU cc_start: 0.8618 (mp0) cc_final: 0.8416 (mp0) REVERT: D 448 TYR cc_start: 0.8551 (t80) cc_final: 0.8258 (t80) REVERT: D 451 TYR cc_start: 0.8407 (t80) cc_final: 0.8174 (t80) REVERT: D 464 ARG cc_start: 0.6937 (ttt180) cc_final: 0.6653 (ttt180) REVERT: D 493 TRP cc_start: 0.7115 (m100) cc_final: 0.6780 (m100) REVERT: D 512 ASP cc_start: 0.5930 (m-30) cc_final: 0.5660 (t0) REVERT: D 553 LEU cc_start: 0.9375 (tt) cc_final: 0.9118 (pp) REVERT: D 557 LEU cc_start: 0.9017 (tt) cc_final: 0.8786 (mm) REVERT: D 574 MET cc_start: 0.7812 (ppp) cc_final: 0.7400 (ppp) REVERT: D 635 LEU cc_start: 0.9049 (mt) cc_final: 0.8836 (mt) REVERT: D 702 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7566 (tm-30) outliers start: 4 outliers final: 0 residues processed: 587 average time/residue: 0.3096 time to fit residues: 282.4728 Evaluate side-chains 397 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.127 ------------------------------------------------------------------------------- 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: 6.9990 chunk 74 optimal weight: 10.0000 chunk 199 optimal weight: 0.0270 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 240 optimal weight: 0.1980 chunk 259 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 overall best weight: 3.6444 ------------------------------------------------------------------------------- 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 274 GLN A 452 ASN 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 21884 Z= 0.245 Angle : 0.771 9.101 29632 Z= 0.395 Chirality : 0.042 0.193 3384 Planarity : 0.004 0.049 3724 Dihedral : 6.306 38.349 2864 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.57 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.50 (0.16), residues: 2636 helix: -0.29 (0.13), residues: 1488 sheet: -4.68 (0.43), residues: 48 loop : -3.56 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 521 HIS 0.006 0.001 HIS B 256 PHE 0.027 0.002 PHE B 124 TYR 0.019 0.002 TYR D 359 ARG 0.008 0.001 ARG D 714 *********************** 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 523 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 523 time to evaluate : 2.670 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: A 124 PHE cc_start: 0.8429 (m-80) cc_final: 0.8204 (m-80) REVERT: A 173 MET cc_start: 0.8280 (mtm) cc_final: 0.7999 (mmm) REVERT: A 301 HIS cc_start: 0.9010 (m170) cc_final: 0.8758 (m-70) REVERT: A 321 TYR cc_start: 0.8346 (t80) cc_final: 0.7931 (t80) REVERT: A 448 TYR cc_start: 0.8822 (t80) cc_final: 0.8616 (t80) REVERT: A 455 LEU cc_start: 0.9200 (tp) cc_final: 0.8741 (tp) REVERT: A 493 TRP cc_start: 0.6953 (m100) cc_final: 0.6750 (m100) REVERT: A 512 ASP cc_start: 0.6299 (m-30) cc_final: 0.5862 (t0) REVERT: A 574 MET cc_start: 0.7843 (ppp) cc_final: 0.7165 (ppp) REVERT: A 578 MET cc_start: 0.8406 (mtp) cc_final: 0.7960 (mtm) REVERT: A 632 LEU cc_start: 0.9447 (mt) cc_final: 0.9247 (mm) REVERT: A 702 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7786 (tm-30) REVERT: B 134 GLU cc_start: 0.8412 (pm20) cc_final: 0.8206 (pm20) REVERT: B 141 ASP cc_start: 0.9083 (m-30) cc_final: 0.8791 (p0) REVERT: B 448 TYR cc_start: 0.8826 (t80) cc_final: 0.7873 (t80) REVERT: B 493 TRP cc_start: 0.7378 (m100) cc_final: 0.6724 (m100) REVERT: B 572 MET cc_start: 0.9297 (mmm) cc_final: 0.9062 (mmm) REVERT: B 574 MET cc_start: 0.7703 (ppp) cc_final: 0.7096 (ppp) REVERT: B 578 MET cc_start: 0.8569 (mtp) cc_final: 0.8183 (mtm) REVERT: C 141 ASP cc_start: 0.9191 (t0) cc_final: 0.8960 (t0) REVERT: C 303 LEU cc_start: 0.9443 (mp) cc_final: 0.9092 (tp) REVERT: C 388 SER cc_start: 0.8398 (m) cc_final: 0.7754 (p) REVERT: C 448 TYR cc_start: 0.8807 (t80) cc_final: 0.8429 (t80) REVERT: C 455 LEU cc_start: 0.9555 (tp) cc_final: 0.9210 (tp) REVERT: C 484 LEU cc_start: 0.8711 (tp) cc_final: 0.8380 (tp) REVERT: C 574 MET cc_start: 0.7700 (ppp) cc_final: 0.6944 (ppp) REVERT: C 578 MET cc_start: 0.8707 (mtp) cc_final: 0.8351 (mtm) REVERT: C 632 LEU cc_start: 0.9311 (mt) cc_final: 0.8963 (mm) REVERT: C 735 ASN cc_start: 0.7618 (m110) cc_final: 0.7324 (m110) REVERT: D 301 HIS cc_start: 0.9000 (m170) cc_final: 0.8697 (m-70) REVERT: D 418 GLU cc_start: 0.8543 (mp0) cc_final: 0.8238 (mp0) REVERT: D 448 TYR cc_start: 0.8915 (t80) cc_final: 0.8633 (t80) REVERT: D 455 LEU cc_start: 0.9315 (tp) cc_final: 0.8836 (tp) REVERT: D 493 TRP cc_start: 0.7103 (m100) cc_final: 0.6226 (m100) REVERT: D 512 ASP cc_start: 0.6242 (m-30) cc_final: 0.5917 (t0) REVERT: D 574 MET cc_start: 0.7835 (ppp) cc_final: 0.6767 (ppp) REVERT: D 578 MET cc_start: 0.8514 (mtp) cc_final: 0.7652 (mtp) REVERT: D 631 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7710 (tm-30) REVERT: D 635 LEU cc_start: 0.9164 (mt) cc_final: 0.8897 (mt) REVERT: D 733 ARG cc_start: 0.7332 (mmm160) cc_final: 0.6939 (mmm160) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.3001 time to fit residues: 246.9231 Evaluate side-chains 370 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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: 7.9990 chunk 180 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 21884 Z= 0.297 Angle : 0.795 10.163 29632 Z= 0.409 Chirality : 0.043 0.170 3384 Planarity : 0.005 0.096 3724 Dihedral : 6.301 38.527 2864 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.57 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.29 (0.16), residues: 2636 helix: -0.12 (0.13), residues: 1508 sheet: -4.25 (0.50), residues: 48 loop : -3.56 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 521 HIS 0.008 0.001 HIS B 256 PHE 0.021 0.002 PHE A 597 TYR 0.020 0.002 TYR D 359 ARG 0.015 0.001 ARG A 714 *********************** 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 496 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.673 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: A 173 MET cc_start: 0.8316 (mtm) cc_final: 0.8085 (mmm) REVERT: A 448 TYR cc_start: 0.9104 (t80) cc_final: 0.8524 (t80) REVERT: A 493 TRP cc_start: 0.6924 (m100) cc_final: 0.6474 (m100) REVERT: A 512 ASP cc_start: 0.6353 (m-30) cc_final: 0.5858 (t0) REVERT: A 574 MET cc_start: 0.7886 (ppp) cc_final: 0.7190 (ppp) REVERT: A 578 MET cc_start: 0.8615 (mtp) cc_final: 0.8374 (mtm) REVERT: A 632 LEU cc_start: 0.9452 (mt) cc_final: 0.9245 (mm) REVERT: A 691 ILE cc_start: 0.9548 (mp) cc_final: 0.8559 (mm) REVERT: B 141 ASP cc_start: 0.9088 (m-30) cc_final: 0.8770 (t0) REVERT: B 448 TYR cc_start: 0.9087 (t80) cc_final: 0.8778 (t80) REVERT: B 453 ILE cc_start: 0.9332 (mm) cc_final: 0.9013 (tp) REVERT: B 493 TRP cc_start: 0.7573 (m100) cc_final: 0.6620 (m100) REVERT: B 529 GLN cc_start: 0.9239 (tp40) cc_final: 0.8963 (tp40) REVERT: B 550 CYS cc_start: 0.8864 (t) cc_final: 0.8638 (t) REVERT: B 574 MET cc_start: 0.7830 (ppp) cc_final: 0.6840 (ppp) REVERT: B 578 MET cc_start: 0.8748 (mtp) cc_final: 0.8450 (mtm) REVERT: C 141 ASP cc_start: 0.9190 (t0) cc_final: 0.8941 (t0) REVERT: C 303 LEU cc_start: 0.9521 (mp) cc_final: 0.9226 (tp) REVERT: C 388 SER cc_start: 0.8377 (m) cc_final: 0.7825 (m) REVERT: C 448 TYR cc_start: 0.9131 (t80) cc_final: 0.8789 (t80) REVERT: C 455 LEU cc_start: 0.9540 (tp) cc_final: 0.9030 (tp) REVERT: C 464 ARG cc_start: 0.6401 (mtt-85) cc_final: 0.5655 (tpt-90) REVERT: C 529 GLN cc_start: 0.9506 (tp40) cc_final: 0.9113 (tp40) REVERT: C 574 MET cc_start: 0.7831 (ppp) cc_final: 0.6598 (ppp) REVERT: C 578 MET cc_start: 0.8757 (mtp) cc_final: 0.8222 (mtm) REVERT: C 632 LEU cc_start: 0.9410 (mt) cc_final: 0.9155 (mm) REVERT: C 672 MET cc_start: 0.8252 (tpt) cc_final: 0.7853 (tpt) REVERT: D 169 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7613 (mtmt) REVERT: D 448 TYR cc_start: 0.9110 (t80) cc_final: 0.8845 (t80) REVERT: D 451 TYR cc_start: 0.8657 (t80) cc_final: 0.8451 (t80) REVERT: D 455 LEU cc_start: 0.9327 (tp) cc_final: 0.9018 (tp) REVERT: D 493 TRP cc_start: 0.7129 (m100) cc_final: 0.6548 (m100) REVERT: D 512 ASP cc_start: 0.6275 (m-30) cc_final: 0.5815 (t0) REVERT: D 548 LEU cc_start: 0.9349 (pt) cc_final: 0.9106 (mm) REVERT: D 550 CYS cc_start: 0.8903 (t) cc_final: 0.8621 (t) REVERT: D 578 MET cc_start: 0.8520 (mtp) cc_final: 0.8206 (mtt) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.2999 time to fit residues: 234.0325 Evaluate side-chains 378 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.570 ------------------------------------------------------------------------------- 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: 3.9990 chunk 144 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21884 Z= 0.251 Angle : 0.768 9.104 29632 Z= 0.392 Chirality : 0.042 0.168 3384 Planarity : 0.004 0.061 3724 Dihedral : 6.127 38.929 2864 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.42 % Favored : 85.43 % 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 : 0.43 % 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: 0.09 (0.13), residues: 1480 sheet: -3.93 (0.55), residues: 48 loop : -3.54 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 742 HIS 0.007 0.001 HIS B 256 PHE 0.030 0.002 PHE C 597 TYR 0.017 0.002 TYR D 359 ARG 0.007 0.000 ARG B 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 500 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 2.750 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 173 MET cc_start: 0.8409 (mtm) cc_final: 0.8017 (mmm) REVERT: A 301 HIS cc_start: 0.9099 (m-70) cc_final: 0.8698 (m-70) REVERT: A 448 TYR cc_start: 0.9124 (t80) cc_final: 0.8587 (t80) REVERT: A 464 ARG cc_start: 0.6976 (ttt180) cc_final: 0.6368 (ttp-170) REVERT: A 493 TRP cc_start: 0.6935 (m100) cc_final: 0.6288 (m100) REVERT: A 512 ASP cc_start: 0.6526 (m-30) cc_final: 0.5894 (t0) REVERT: A 574 MET cc_start: 0.7824 (ppp) cc_final: 0.7165 (ppp) REVERT: A 578 MET cc_start: 0.8598 (mtp) cc_final: 0.7899 (mtm) REVERT: A 668 LEU cc_start: 0.9385 (mm) cc_final: 0.9104 (mm) REVERT: B 141 ASP cc_start: 0.9039 (m-30) cc_final: 0.8745 (t0) REVERT: B 323 MET cc_start: 0.7909 (tpt) cc_final: 0.7442 (tpt) REVERT: B 388 SER cc_start: 0.8373 (m) cc_final: 0.7888 (p) REVERT: B 401 ASN cc_start: 0.8144 (t0) cc_final: 0.7936 (t0) REVERT: B 448 TYR cc_start: 0.9109 (t80) cc_final: 0.8695 (t80) REVERT: B 455 LEU cc_start: 0.9460 (tp) cc_final: 0.9084 (tp) REVERT: B 493 TRP cc_start: 0.7579 (m100) cc_final: 0.6609 (m100) REVERT: B 529 GLN cc_start: 0.9180 (tp40) cc_final: 0.8922 (tp40) REVERT: B 574 MET cc_start: 0.7659 (ppp) cc_final: 0.6819 (ppp) REVERT: B 578 MET cc_start: 0.8604 (mtp) cc_final: 0.7915 (mtm) REVERT: C 141 ASP cc_start: 0.9192 (t0) cc_final: 0.8938 (t0) REVERT: C 388 SER cc_start: 0.8413 (m) cc_final: 0.7609 (m) REVERT: C 448 TYR cc_start: 0.9163 (t80) cc_final: 0.8715 (t80) REVERT: C 453 ILE cc_start: 0.9307 (mm) cc_final: 0.9052 (tp) REVERT: C 464 ARG cc_start: 0.6241 (mtt-85) cc_final: 0.5664 (tpt-90) REVERT: C 488 MET cc_start: 0.8379 (ppp) cc_final: 0.8108 (ppp) REVERT: C 529 GLN cc_start: 0.9449 (tp40) cc_final: 0.9027 (tp40) REVERT: C 574 MET cc_start: 0.7777 (ppp) cc_final: 0.7264 (ppp) REVERT: C 632 LEU cc_start: 0.9413 (mt) cc_final: 0.9137 (mm) REVERT: D 301 HIS cc_start: 0.9077 (m170) cc_final: 0.8603 (m90) REVERT: D 336 MET cc_start: 0.7019 (tmm) cc_final: 0.6765 (tmm) REVERT: D 448 TYR cc_start: 0.9083 (t80) cc_final: 0.8755 (t80) REVERT: D 493 TRP cc_start: 0.7213 (m100) cc_final: 0.6610 (m100) REVERT: D 512 ASP cc_start: 0.6384 (m-30) cc_final: 0.5903 (t0) REVERT: D 548 LEU cc_start: 0.9370 (pt) cc_final: 0.9099 (mt) REVERT: D 578 MET cc_start: 0.8539 (mtp) cc_final: 0.7963 (mtt) REVERT: D 631 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7377 (tm-30) REVERT: D 635 LEU cc_start: 0.9132 (mt) cc_final: 0.8814 (mt) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.3069 time to fit residues: 245.3423 Evaluate side-chains 385 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.680 ------------------------------------------------------------------------------- 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: 3.9990 chunk 229 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 0.0470 chunk 255 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21884 Z= 0.176 Angle : 0.763 10.432 29632 Z= 0.377 Chirality : 0.041 0.195 3384 Planarity : 0.004 0.066 3724 Dihedral : 5.741 34.816 2864 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.67 % Favored : 87.18 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -1.95 (0.16), residues: 2636 helix: 0.26 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -3.50 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 742 HIS 0.004 0.001 HIS C 417 PHE 0.031 0.001 PHE C 597 TYR 0.016 0.001 TYR C 650 ARG 0.018 0.001 ARG A 464 *********************** 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 531 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 2.585 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 301 HIS cc_start: 0.8997 (m-70) cc_final: 0.8538 (m-70) REVERT: A 448 TYR cc_start: 0.9101 (t80) cc_final: 0.8511 (t80) REVERT: A 484 LEU cc_start: 0.8512 (tp) cc_final: 0.8244 (pp) REVERT: A 488 MET cc_start: 0.8201 (ppp) cc_final: 0.7947 (ppp) REVERT: A 493 TRP cc_start: 0.6832 (m100) cc_final: 0.6338 (m100) REVERT: A 512 ASP cc_start: 0.6406 (m-30) cc_final: 0.5802 (t0) REVERT: A 548 LEU cc_start: 0.9045 (pt) cc_final: 0.8699 (mm) REVERT: A 574 MET cc_start: 0.7786 (ppp) cc_final: 0.6973 (ppp) REVERT: A 578 MET cc_start: 0.8602 (mtp) cc_final: 0.7900 (mtm) REVERT: A 594 TYR cc_start: 0.7368 (t80) cc_final: 0.6744 (t80) REVERT: A 669 LEU cc_start: 0.9371 (mm) cc_final: 0.9159 (tp) REVERT: A 672 MET cc_start: 0.8075 (tpt) cc_final: 0.7816 (tpt) REVERT: B 122 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7656 (mmm160) REVERT: B 141 ASP cc_start: 0.9015 (m-30) cc_final: 0.8702 (t0) REVERT: B 318 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8425 (tppt) REVERT: B 388 SER cc_start: 0.8152 (m) cc_final: 0.7722 (p) REVERT: B 448 TYR cc_start: 0.9123 (t80) cc_final: 0.8693 (t80) REVERT: B 455 LEU cc_start: 0.9341 (tp) cc_final: 0.9120 (tp) REVERT: B 484 LEU cc_start: 0.8644 (tp) cc_final: 0.8364 (pp) REVERT: B 493 TRP cc_start: 0.7414 (m100) cc_final: 0.6584 (m100) REVERT: B 529 GLN cc_start: 0.9072 (tp40) cc_final: 0.8637 (tp40) REVERT: B 574 MET cc_start: 0.7629 (ppp) cc_final: 0.6807 (ppp) REVERT: B 578 MET cc_start: 0.8663 (mtp) cc_final: 0.8041 (mtm) REVERT: B 601 PHE cc_start: 0.8302 (m-80) cc_final: 0.8099 (m-80) REVERT: B 632 LEU cc_start: 0.9248 (mt) cc_final: 0.8949 (mm) REVERT: C 141 ASP cc_start: 0.9124 (t0) cc_final: 0.8864 (t0) REVERT: C 388 SER cc_start: 0.8145 (m) cc_final: 0.7432 (m) REVERT: C 429 LEU cc_start: 0.9356 (mm) cc_final: 0.9147 (tt) REVERT: C 448 TYR cc_start: 0.9256 (t80) cc_final: 0.8825 (t80) REVERT: C 453 ILE cc_start: 0.9183 (mm) cc_final: 0.8938 (tp) REVERT: C 529 GLN cc_start: 0.9364 (tp40) cc_final: 0.8936 (tp40) REVERT: C 574 MET cc_start: 0.7677 (ppp) cc_final: 0.7191 (ppp) REVERT: C 632 LEU cc_start: 0.9302 (mt) cc_final: 0.9101 (mm) REVERT: C 672 MET cc_start: 0.8141 (tpt) cc_final: 0.7713 (tpt) REVERT: D 301 HIS cc_start: 0.8950 (m170) cc_final: 0.8672 (m-70) REVERT: D 448 TYR cc_start: 0.9072 (t80) cc_final: 0.8771 (t80) REVERT: D 493 TRP cc_start: 0.7004 (m100) cc_final: 0.6185 (m100) REVERT: D 512 ASP cc_start: 0.6271 (m-30) cc_final: 0.5811 (t0) REVERT: D 548 LEU cc_start: 0.9210 (pt) cc_final: 0.8936 (mt) REVERT: D 555 MET cc_start: 0.8800 (tpp) cc_final: 0.8365 (tpp) REVERT: D 574 MET cc_start: 0.7634 (ppp) cc_final: 0.6825 (ppp) REVERT: D 578 MET cc_start: 0.8518 (mtp) cc_final: 0.7972 (mtm) REVERT: D 614 LYS cc_start: 0.6915 (tppt) cc_final: 0.6384 (pttm) REVERT: D 632 LEU cc_start: 0.9455 (mt) cc_final: 0.9224 (mt) REVERT: D 661 TYR cc_start: 0.8348 (t80) cc_final: 0.7969 (t80) REVERT: D 669 LEU cc_start: 0.9395 (mm) cc_final: 0.9013 (tp) REVERT: D 733 ARG cc_start: 0.7107 (mmm160) cc_final: 0.6767 (mmm160) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.3115 time to fit residues: 266.9153 Evaluate side-chains 397 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.700 ------------------------------------------------------------------------------- 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: 8.9990 chunk 28 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21884 Z= 0.201 Angle : 0.751 10.508 29632 Z= 0.374 Chirality : 0.041 0.176 3384 Planarity : 0.005 0.086 3724 Dihedral : 5.732 33.582 2864 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.51 % Favored : 86.34 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -1.92 (0.16), residues: 2636 helix: 0.29 (0.13), residues: 1464 sheet: -4.00 (0.54), residues: 48 loop : -3.43 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 742 HIS 0.004 0.001 HIS A 160 PHE 0.029 0.001 PHE C 597 TYR 0.017 0.001 TYR A 594 ARG 0.017 0.000 ARG D 118 *********************** 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 491 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.9012 (m-70) cc_final: 0.8615 (m-70) REVERT: A 336 MET cc_start: 0.7849 (ptm) cc_final: 0.7623 (ptp) REVERT: A 448 TYR cc_start: 0.9129 (t80) cc_final: 0.8695 (t80) REVERT: A 493 TRP cc_start: 0.6947 (m100) cc_final: 0.6457 (m100) REVERT: A 512 ASP cc_start: 0.6552 (m-30) cc_final: 0.5892 (t0) REVERT: A 548 LEU cc_start: 0.8986 (pt) cc_final: 0.8774 (mm) REVERT: A 574 MET cc_start: 0.7725 (ppp) cc_final: 0.6973 (ppp) REVERT: A 578 MET cc_start: 0.8613 (mtp) cc_final: 0.8059 (mtm) REVERT: A 730 LEU cc_start: 0.9244 (pt) cc_final: 0.9039 (pt) REVERT: B 141 ASP cc_start: 0.9006 (m-30) cc_final: 0.8687 (t0) REVERT: B 388 SER cc_start: 0.8319 (m) cc_final: 0.7263 (p) REVERT: B 448 TYR cc_start: 0.9207 (t80) cc_final: 0.8656 (t80) REVERT: B 484 LEU cc_start: 0.8607 (tp) cc_final: 0.8348 (pp) REVERT: B 493 TRP cc_start: 0.7390 (m100) cc_final: 0.6524 (m100) REVERT: B 529 GLN cc_start: 0.9157 (tp40) cc_final: 0.8551 (tp40) REVERT: B 557 LEU cc_start: 0.9163 (tp) cc_final: 0.8897 (tp) REVERT: B 574 MET cc_start: 0.7706 (ppp) cc_final: 0.6824 (ppp) REVERT: B 578 MET cc_start: 0.8594 (mtp) cc_final: 0.7938 (mtm) REVERT: B 598 LEU cc_start: 0.9492 (pp) cc_final: 0.9229 (mt) REVERT: B 632 LEU cc_start: 0.9447 (mt) cc_final: 0.9233 (mm) REVERT: C 141 ASP cc_start: 0.9199 (t0) cc_final: 0.8908 (t0) REVERT: C 388 SER cc_start: 0.8115 (m) cc_final: 0.7340 (m) REVERT: C 453 ILE cc_start: 0.9138 (mm) cc_final: 0.8895 (tp) REVERT: C 464 ARG cc_start: 0.6028 (mtt-85) cc_final: 0.5670 (tpt-90) REVERT: C 529 GLN cc_start: 0.9422 (tp40) cc_final: 0.8931 (tp40) REVERT: C 574 MET cc_start: 0.7758 (ppp) cc_final: 0.6689 (ppp) REVERT: C 578 MET cc_start: 0.8747 (mtp) cc_final: 0.8382 (mtm) REVERT: C 632 LEU cc_start: 0.9348 (mt) cc_final: 0.9101 (mm) REVERT: C 730 LEU cc_start: 0.9117 (pt) cc_final: 0.8893 (pt) REVERT: D 301 HIS cc_start: 0.8929 (m170) cc_final: 0.8626 (m-70) REVERT: D 318 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8479 (tppt) REVERT: D 448 TYR cc_start: 0.9133 (t80) cc_final: 0.8853 (t80) REVERT: D 512 ASP cc_start: 0.6389 (m-30) cc_final: 0.5869 (t0) REVERT: D 548 LEU cc_start: 0.9237 (pt) cc_final: 0.8949 (mt) REVERT: D 574 MET cc_start: 0.7611 (ppp) cc_final: 0.6270 (ppp) REVERT: D 578 MET cc_start: 0.8560 (mtp) cc_final: 0.7944 (mtt) REVERT: D 614 LYS cc_start: 0.6850 (tppt) cc_final: 0.6163 (ptpp) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.2979 time to fit residues: 236.8369 Evaluate side-chains 384 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.723 ------------------------------------------------------------------------------- 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: 9.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 200 optimal weight: 30.0000 chunk 231 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21884 Z= 0.222 Angle : 0.760 11.222 29632 Z= 0.380 Chirality : 0.042 0.202 3384 Planarity : 0.004 0.071 3724 Dihedral : 5.747 32.205 2864 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.15 % Favored : 85.70 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: -1.97 (0.16), residues: 2636 helix: 0.16 (0.13), residues: 1460 sheet: -3.95 (0.57), residues: 48 loop : -3.31 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 493 HIS 0.004 0.001 HIS C 301 PHE 0.030 0.001 PHE C 597 TYR 0.018 0.001 TYR B 359 ARG 0.007 0.000 ARG B 118 *********************** 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 : 2.810 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 301 HIS cc_start: 0.9027 (m-70) cc_final: 0.8623 (m-70) REVERT: A 318 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8535 (tppt) REVERT: A 336 MET cc_start: 0.7939 (ptm) cc_final: 0.7652 (ptp) REVERT: A 448 TYR cc_start: 0.9126 (t80) cc_final: 0.8640 (t80) REVERT: A 493 TRP cc_start: 0.7112 (m100) cc_final: 0.6407 (m100) REVERT: A 512 ASP cc_start: 0.6488 (m-30) cc_final: 0.5901 (t0) REVERT: A 578 MET cc_start: 0.8633 (mtp) cc_final: 0.8135 (mtm) REVERT: A 594 TYR cc_start: 0.7193 (t80) cc_final: 0.6961 (t80) REVERT: B 141 ASP cc_start: 0.9015 (m-30) cc_final: 0.8697 (t70) REVERT: B 318 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8624 (tppp) REVERT: B 388 SER cc_start: 0.8494 (m) cc_final: 0.7262 (p) REVERT: B 464 ARG cc_start: 0.7592 (ptp-170) cc_final: 0.7149 (ptp-170) REVERT: B 484 LEU cc_start: 0.8626 (tp) cc_final: 0.8346 (pp) REVERT: B 529 GLN cc_start: 0.9162 (tp40) cc_final: 0.8526 (tp40) REVERT: B 550 CYS cc_start: 0.8869 (t) cc_final: 0.8625 (t) REVERT: B 557 LEU cc_start: 0.9140 (tp) cc_final: 0.8794 (tp) REVERT: B 574 MET cc_start: 0.7723 (ppp) cc_final: 0.6959 (ppp) REVERT: B 578 MET cc_start: 0.8609 (mtp) cc_final: 0.8095 (mtm) REVERT: B 598 LEU cc_start: 0.9500 (pp) cc_final: 0.9300 (mt) REVERT: B 601 PHE cc_start: 0.8226 (m-80) cc_final: 0.7546 (m-80) REVERT: B 632 LEU cc_start: 0.9464 (mt) cc_final: 0.9262 (mm) REVERT: B 665 THR cc_start: 0.9066 (p) cc_final: 0.8865 (p) REVERT: C 141 ASP cc_start: 0.9202 (t0) cc_final: 0.8897 (t0) REVERT: C 388 SER cc_start: 0.8049 (m) cc_final: 0.7080 (m) REVERT: C 455 LEU cc_start: 0.9266 (tp) cc_final: 0.8972 (tp) REVERT: C 464 ARG cc_start: 0.6252 (mtt-85) cc_final: 0.5789 (tpt-90) REVERT: C 529 GLN cc_start: 0.9437 (tp40) cc_final: 0.8883 (tp40) REVERT: C 574 MET cc_start: 0.7771 (ppp) cc_final: 0.6703 (ppp) REVERT: C 578 MET cc_start: 0.8705 (mtp) cc_final: 0.8240 (mtm) REVERT: C 632 LEU cc_start: 0.9376 (mt) cc_final: 0.9134 (mm) REVERT: D 301 HIS cc_start: 0.8921 (m170) cc_final: 0.8652 (m-70) REVERT: D 318 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8475 (tppt) REVERT: D 448 TYR cc_start: 0.9125 (t80) cc_final: 0.8884 (t80) REVERT: D 493 TRP cc_start: 0.7474 (m100) cc_final: 0.6679 (m100) REVERT: D 512 ASP cc_start: 0.6307 (m-30) cc_final: 0.5726 (t0) REVERT: D 548 LEU cc_start: 0.9232 (pt) cc_final: 0.8954 (mt) REVERT: D 555 MET cc_start: 0.8772 (tpp) cc_final: 0.8384 (tpt) REVERT: D 578 MET cc_start: 0.8492 (mtp) cc_final: 0.8091 (mtt) REVERT: D 614 LYS cc_start: 0.6940 (tppt) cc_final: 0.6314 (ptpp) REVERT: D 632 LEU cc_start: 0.9448 (mt) cc_final: 0.9097 (mt) REVERT: D 661 TYR cc_start: 0.8410 (t80) cc_final: 0.7642 (t80) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.2892 time to fit residues: 225.1395 Evaluate side-chains 383 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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: 2.9990 chunk 222 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 20.0000 chunk 155 optimal weight: 0.1980 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 580 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN D 580 GLN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21884 Z= 0.250 Angle : 0.783 11.170 29632 Z= 0.391 Chirality : 0.042 0.167 3384 Planarity : 0.004 0.072 3724 Dihedral : 5.803 32.345 2864 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.02 % Favored : 84.83 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -1.90 (0.17), residues: 2636 helix: 0.25 (0.13), residues: 1472 sheet: -3.79 (0.61), residues: 48 loop : -3.38 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 739 HIS 0.007 0.001 HIS C 301 PHE 0.031 0.002 PHE C 597 TYR 0.015 0.002 TYR A 661 ARG 0.008 0.000 ARG D 733 *********************** 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 464 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 2.515 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: A 159 MET cc_start: 0.8556 (mmt) cc_final: 0.8221 (mmm) REVERT: A 301 HIS cc_start: 0.9013 (m-70) cc_final: 0.8618 (m-70) REVERT: A 318 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8560 (tppt) REVERT: A 336 MET cc_start: 0.7957 (ptm) cc_final: 0.7662 (ptp) REVERT: A 493 TRP cc_start: 0.7062 (m100) cc_final: 0.6643 (m100) REVERT: A 572 MET cc_start: 0.8650 (mmm) cc_final: 0.8321 (mmm) REVERT: A 578 MET cc_start: 0.8517 (mtp) cc_final: 0.8154 (mtm) REVERT: B 141 ASP cc_start: 0.9017 (m-30) cc_final: 0.8697 (t0) REVERT: B 318 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8615 (tppp) REVERT: B 380 TRP cc_start: 0.7459 (t-100) cc_final: 0.7143 (t-100) REVERT: B 388 SER cc_start: 0.8494 (m) cc_final: 0.7374 (m) REVERT: B 484 LEU cc_start: 0.8663 (tp) cc_final: 0.8346 (pp) REVERT: B 493 TRP cc_start: 0.7042 (m100) cc_final: 0.6657 (m100) REVERT: B 529 GLN cc_start: 0.9238 (tp40) cc_final: 0.8526 (tp40) REVERT: B 550 CYS cc_start: 0.8887 (t) cc_final: 0.8668 (t) REVERT: B 557 LEU cc_start: 0.9229 (tp) cc_final: 0.8816 (tp) REVERT: B 578 MET cc_start: 0.8645 (mtp) cc_final: 0.8274 (mtm) REVERT: C 141 ASP cc_start: 0.9194 (t0) cc_final: 0.8892 (t0) REVERT: C 388 SER cc_start: 0.8143 (m) cc_final: 0.7069 (m) REVERT: C 464 ARG cc_start: 0.6278 (mtt-85) cc_final: 0.5844 (tpt-90) REVERT: C 529 GLN cc_start: 0.9447 (tp40) cc_final: 0.8837 (tp40) REVERT: C 557 LEU cc_start: 0.9256 (tp) cc_final: 0.8990 (tp) REVERT: C 574 MET cc_start: 0.7772 (ppp) cc_final: 0.6691 (ppp) REVERT: C 578 MET cc_start: 0.8722 (mtp) cc_final: 0.8108 (mtm) REVERT: C 632 LEU cc_start: 0.9408 (mt) cc_final: 0.9136 (mm) REVERT: C 672 MET cc_start: 0.7963 (tpt) cc_final: 0.7630 (tpt) REVERT: C 730 LEU cc_start: 0.9124 (pt) cc_final: 0.8907 (pt) REVERT: D 301 HIS cc_start: 0.8891 (m170) cc_final: 0.8689 (m-70) REVERT: D 318 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8528 (tppt) REVERT: D 373 LEU cc_start: 0.9287 (mt) cc_final: 0.8403 (mt) REVERT: D 448 TYR cc_start: 0.9094 (t80) cc_final: 0.8829 (t80) REVERT: D 493 TRP cc_start: 0.7521 (m100) cc_final: 0.6732 (m100) REVERT: D 512 ASP cc_start: 0.6376 (m-30) cc_final: 0.5773 (t0) REVERT: D 548 LEU cc_start: 0.9206 (pt) cc_final: 0.8944 (mt) REVERT: D 555 MET cc_start: 0.8810 (tpp) cc_final: 0.8526 (tpt) REVERT: D 578 MET cc_start: 0.8567 (mtp) cc_final: 0.8069 (mtt) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.2875 time to fit residues: 213.6802 Evaluate side-chains 372 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.509 ------------------------------------------------------------------------------- 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: 7.9990 chunk 153 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 174 optimal weight: 0.0980 chunk 263 optimal weight: 8.9990 chunk 242 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 0.0870 chunk 128 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 580 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21884 Z= 0.217 Angle : 0.781 11.007 29632 Z= 0.387 Chirality : 0.042 0.189 3384 Planarity : 0.004 0.076 3724 Dihedral : 5.726 31.790 2864 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.76 % Favored : 85.09 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -1.87 (0.17), residues: 2636 helix: 0.28 (0.13), residues: 1460 sheet: -3.80 (0.62), residues: 48 loop : -3.32 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 493 HIS 0.014 0.001 HIS C 417 PHE 0.025 0.001 PHE C 597 TYR 0.035 0.001 TYR A 594 ARG 0.008 0.000 ARG D 733 ********************** 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 466 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 2.587 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 301 HIS cc_start: 0.8978 (m-70) cc_final: 0.8417 (m90) REVERT: A 318 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8534 (tppt) REVERT: A 336 MET cc_start: 0.7935 (ptm) cc_final: 0.7715 (ptm) REVERT: A 448 TYR cc_start: 0.9123 (t80) cc_final: 0.8828 (t80) REVERT: A 493 TRP cc_start: 0.7146 (m100) cc_final: 0.6451 (m100) REVERT: A 572 MET cc_start: 0.8667 (mmm) cc_final: 0.8317 (mmm) REVERT: A 578 MET cc_start: 0.8565 (mtp) cc_final: 0.8281 (mtm) REVERT: B 141 ASP cc_start: 0.8982 (m-30) cc_final: 0.8664 (t0) REVERT: B 318 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8581 (tppp) REVERT: B 380 TRP cc_start: 0.7373 (t-100) cc_final: 0.7053 (t-100) REVERT: B 388 SER cc_start: 0.8432 (m) cc_final: 0.7106 (m) REVERT: B 440 MET cc_start: 0.8306 (mmp) cc_final: 0.8072 (mmp) REVERT: B 484 LEU cc_start: 0.8506 (tp) cc_final: 0.8225 (pp) REVERT: B 529 GLN cc_start: 0.9205 (tp40) cc_final: 0.8553 (tp40) REVERT: B 557 LEU cc_start: 0.9208 (tp) cc_final: 0.8818 (tp) REVERT: B 578 MET cc_start: 0.8597 (mtp) cc_final: 0.8045 (mtm) REVERT: B 665 THR cc_start: 0.9133 (p) cc_final: 0.8799 (p) REVERT: C 141 ASP cc_start: 0.9189 (t0) cc_final: 0.8885 (t0) REVERT: C 388 SER cc_start: 0.8038 (m) cc_final: 0.6879 (m) REVERT: C 464 ARG cc_start: 0.6262 (mtt-85) cc_final: 0.5845 (tpt-90) REVERT: C 529 GLN cc_start: 0.9411 (tp40) cc_final: 0.8842 (tp40) REVERT: C 557 LEU cc_start: 0.9238 (tp) cc_final: 0.8951 (tp) REVERT: C 574 MET cc_start: 0.7809 (ppp) cc_final: 0.6669 (ppp) REVERT: C 578 MET cc_start: 0.8672 (mtp) cc_final: 0.8166 (mtm) REVERT: C 632 LEU cc_start: 0.9372 (mt) cc_final: 0.9140 (mm) REVERT: C 642 LEU cc_start: 0.9057 (mt) cc_final: 0.8840 (mp) REVERT: C 672 MET cc_start: 0.7967 (tpt) cc_final: 0.7521 (tpt) REVERT: D 301 HIS cc_start: 0.8877 (m170) cc_final: 0.8671 (m-70) REVERT: D 318 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8500 (tppt) REVERT: D 373 LEU cc_start: 0.9267 (mt) cc_final: 0.8411 (mt) REVERT: D 401 ASN cc_start: 0.8250 (t0) cc_final: 0.7907 (t0) REVERT: D 488 MET cc_start: 0.8179 (ppp) cc_final: 0.7956 (ppp) REVERT: D 493 TRP cc_start: 0.7529 (m100) cc_final: 0.6607 (m100) REVERT: D 512 ASP cc_start: 0.6368 (m-30) cc_final: 0.5761 (t0) REVERT: D 548 LEU cc_start: 0.9190 (pt) cc_final: 0.8968 (mt) REVERT: D 555 MET cc_start: 0.8774 (tpp) cc_final: 0.8465 (tpt) REVERT: D 578 MET cc_start: 0.8588 (mtp) cc_final: 0.8070 (mtm) REVERT: D 598 LEU cc_start: 0.9417 (mt) cc_final: 0.9001 (mt) REVERT: D 614 LYS cc_start: 0.7106 (tppt) cc_final: 0.6524 (ptpp) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.2909 time to fit residues: 216.7096 Evaluate side-chains 376 residues out of total 2360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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: 0.6980 chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 30 optimal weight: 0.0270 chunk 58 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 184 optimal weight: 0.4980 overall best weight: 2.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.081501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.064234 restraints weight = 88243.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065979 restraints weight = 60815.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067119 restraints weight = 45496.261| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21884 Z= 0.193 Angle : 0.779 13.245 29632 Z= 0.381 Chirality : 0.042 0.192 3384 Planarity : 0.004 0.074 3724 Dihedral : 5.583 31.420 2864 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.45 % Favored : 85.39 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -1.86 (0.17), residues: 2636 helix: 0.30 (0.13), residues: 1456 sheet: -3.70 (0.60), residues: 48 loop : -3.32 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 493 HIS 0.007 0.001 HIS C 417 PHE 0.029 0.001 PHE C 597 TYR 0.030 0.001 TYR A 594 ARG 0.008 0.000 ARG D 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4727.70 seconds wall clock time: 85 minutes 13.04 seconds (5113.04 seconds total)