Starting phenix.real_space_refine on Fri Mar 15 10:02:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/03_2024/6p46_20244.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/03_2024/6p46_20244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/03_2024/6p46_20244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/03_2024/6p46_20244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/03_2024/6p46_20244.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p46_20244/03_2024/6p46_20244.pdb" } resolution = 3.5 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= 0.000 sd= 0.006 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 Ca 2 9.91 5 S 78 5.16 5 C 7508 2.51 5 N 1824 2.21 5 O 1966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 54": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A ARG 808": "NH1" <-> "NH2" Residue "A ARG 810": "NH1" <-> "NH2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 542": "NH1" <-> "NH2" Residue "B GLU 548": "OE1" <-> "OE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B GLU 717": "OE1" <-> "OE2" Residue "B ARG 808": "NH1" <-> "NH2" Residue "B ARG 810": "NH1" <-> "NH2" Residue "B PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B ARG 870": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11378 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5688 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5688 Classifications: {'peptide': 690} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 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: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.08, per 1000 atoms: 0.53 Number of scatterers: 11378 At special positions: 0 Unit cell: (81.543, 128.139, 111.195, 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) Ca 2 19.99 S 78 16.00 O 1966 8.00 N 1824 7.00 C 7508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=1.56 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=1.89 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=1.32 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=1.56 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=1.89 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=1.32 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 2.1 seconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 58.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.911A pdb=" N THR A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.718A pdb=" N VAL A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 4.608A pdb=" N ARG A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 237' Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.534A pdb=" N ARG A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.687A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 312 removed outlier: 3.906A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 306 " --> pdb=" O TRP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 4.101A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 369 removed outlier: 3.852A pdb=" N CYS A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 408 removed outlier: 4.134A pdb=" N VAL A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 489 removed outlier: 3.683A pdb=" N PHE A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TRP A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 486 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.914A pdb=" N SER A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 572 removed outlier: 3.917A pdb=" N MET A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.618A pdb=" N LEU A 588 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 614 removed outlier: 3.661A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 638 removed outlier: 3.843A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix removed outlier: 3.659A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.508A pdb=" N GLN A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 removed outlier: 4.205A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.972A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 748 removed outlier: 3.767A pdb=" N ILE A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.759A pdb=" N TYR A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 856 removed outlier: 3.788A pdb=" N SER A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 131 through 140 removed outlier: 3.911A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.717A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.608A pdb=" N ARG B 235 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 237' Processing helix chain 'B' and resid 266 through 273 removed outlier: 3.533A pdb=" N ARG B 271 " --> pdb=" O TYR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.687A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 removed outlier: 3.905A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 306 " --> pdb=" O TRP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 327 removed outlier: 4.101A pdb=" N PHE B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 369 removed outlier: 3.852A pdb=" N CYS B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 408 removed outlier: 4.133A pdb=" N VAL B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 489 removed outlier: 3.682A pdb=" N PHE B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 486 " --> pdb=" O PHE B 482 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.914A pdb=" N SER B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 572 removed outlier: 3.916A pdb=" N MET B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.619A pdb=" N LEU B 588 " --> pdb=" O VAL B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 3.662A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 3.844A pdb=" N ASN B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 638 removed outlier: 3.658A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 656 removed outlier: 3.508A pdb=" N GLN B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 4.206A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.972A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 707 " --> pdb=" O ASP B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 748 removed outlier: 3.766A pdb=" N ILE B 734 " --> pdb=" O GLN B 730 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.759A pdb=" N TYR B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 856 removed outlier: 3.788A pdb=" N SER B 854 " --> pdb=" O LYS B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 867 through 871 494 hydrogen bonds defined for protein. 1464 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: 2.63 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3090 1.33 - 1.45: 2506 1.45 - 1.57: 5970 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 11686 Sorted by residual: bond pdb=" CA ASP A 375 " pdb=" C ASP A 375 " ideal model delta sigma weight residual 1.527 1.567 -0.041 1.21e-02 6.83e+03 1.14e+01 bond pdb=" CA ASP B 375 " pdb=" C ASP B 375 " ideal model delta sigma weight residual 1.527 1.567 -0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" CA ALA B 571 " pdb=" C ALA B 571 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.34e-02 5.57e+03 1.01e+01 bond pdb=" CA ALA A 571 " pdb=" C ALA A 571 " ideal model delta sigma weight residual 1.523 1.565 -0.042 1.34e-02 5.57e+03 9.92e+00 bond pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.31e+00 ... (remaining 11681 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.25: 220 104.25 - 111.81: 4972 111.81 - 119.37: 4502 119.37 - 126.92: 5957 126.92 - 134.48: 181 Bond angle restraints: 15832 Sorted by residual: angle pdb=" N ALA B 683 " pdb=" CA ALA B 683 " pdb=" C ALA B 683 " ideal model delta sigma weight residual 112.93 96.70 16.23 1.33e+00 5.65e-01 1.49e+02 angle pdb=" N ALA A 683 " pdb=" CA ALA A 683 " pdb=" C ALA A 683 " ideal model delta sigma weight residual 112.93 96.73 16.20 1.33e+00 5.65e-01 1.48e+02 angle pdb=" N LYS B 335 " pdb=" CA LYS B 335 " pdb=" C LYS B 335 " ideal model delta sigma weight residual 112.68 100.25 12.43 1.33e+00 5.65e-01 8.73e+01 angle pdb=" N LYS A 335 " pdb=" CA LYS A 335 " pdb=" C LYS A 335 " ideal model delta sigma weight residual 112.68 100.28 12.40 1.33e+00 5.65e-01 8.69e+01 angle pdb=" N ILE B 622 " pdb=" CA ILE B 622 " pdb=" C ILE B 622 " ideal model delta sigma weight residual 111.90 104.77 7.13 8.10e-01 1.52e+00 7.75e+01 ... (remaining 15827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5906 17.09 - 34.17: 744 34.17 - 51.26: 168 51.26 - 68.35: 42 68.35 - 85.43: 16 Dihedral angle restraints: 6876 sinusoidal: 2800 harmonic: 4076 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual -86.00 -159.23 73.23 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual -86.00 -159.23 73.23 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual 93.00 37.09 55.91 1 1.00e+01 1.00e-02 4.22e+01 ... (remaining 6873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1489 0.100 - 0.200: 189 0.200 - 0.301: 32 0.301 - 0.401: 24 0.401 - 0.501: 4 Chirality restraints: 1738 Sorted by residual: chirality pdb=" CA PHE A 577 " pdb=" N PHE A 577 " pdb=" C PHE A 577 " pdb=" CB PHE A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA PHE B 577 " pdb=" N PHE B 577 " pdb=" C PHE B 577 " pdb=" CB PHE B 577 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA ASN A 330 " pdb=" N ASN A 330 " pdb=" C ASN A 330 " pdb=" CB ASN A 330 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 1735 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 599 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C GLY A 599 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY A 599 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY A 600 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 599 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY B 599 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY B 599 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY B 600 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 570 " -0.022 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C ILE A 570 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 570 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA A 571 " -0.025 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 80 2.42 - 3.04: 6753 3.04 - 3.66: 17729 3.66 - 4.28: 25929 4.28 - 4.90: 41569 Nonbonded interactions: 92060 Sorted by model distance: nonbonded pdb=" C GLU B 594 " pdb=" OE1 GLU B 595 " model vdw 1.800 3.270 nonbonded pdb=" C GLU A 594 " pdb=" OE1 GLU A 595 " model vdw 1.800 3.270 nonbonded pdb=" OE1 GLU A 624 " pdb="CA CA A1001 " model vdw 2.034 2.510 nonbonded pdb=" OE1 GLU B 624 " pdb="CA CA B1001 " model vdw 2.035 2.510 nonbonded pdb=" N GLU B 595 " pdb=" OE1 GLU B 595 " model vdw 2.079 2.520 ... (remaining 92055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.250 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.580 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 : 0.009 0.085 11686 Z= 0.590 Angle : 1.434 16.232 15832 Z= 0.886 Chirality : 0.084 0.501 1738 Planarity : 0.010 0.101 1944 Dihedral : 16.158 85.434 4234 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 3.71 % Allowed : 11.85 % Favored : 84.44 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.45 (0.16), residues: 1344 helix: -3.36 (0.14), residues: 724 sheet: None (None), residues: 0 loop : -3.94 (0.18), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 397 HIS 0.005 0.002 HIS A 830 PHE 0.025 0.003 PHE B 760 TYR 0.034 0.003 TYR A 809 ARG 0.008 0.001 ARG B 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 280 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8792 (mp) REVERT: A 534 MET cc_start: 0.7302 (mmt) cc_final: 0.7087 (mmt) REVERT: A 546 ASP cc_start: 0.7978 (t0) cc_final: 0.7654 (t70) REVERT: A 618 ILE cc_start: 0.9052 (mm) cc_final: 0.8779 (mt) REVERT: B 224 VAL cc_start: 0.1020 (OUTLIER) cc_final: 0.0750 (t) REVERT: B 305 TYR cc_start: 0.7810 (t80) cc_final: 0.7366 (t80) REVERT: B 348 MET cc_start: 0.7175 (mpp) cc_final: 0.6651 (mmm) REVERT: B 523 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8735 (mp) REVERT: B 546 ASP cc_start: 0.7936 (t0) cc_final: 0.7646 (t0) REVERT: B 555 MET cc_start: 0.7960 (tpp) cc_final: 0.7733 (tpt) REVERT: B 855 TYR cc_start: 0.7063 (t80) cc_final: 0.6777 (t80) outliers start: 46 outliers final: 25 residues processed: 323 average time/residue: 0.2355 time to fit residues: 107.2758 Evaluate side-chains 230 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 866 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 283 GLN A 328 GLN A 544 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN A 740 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 275 HIS B 283 GLN B 328 GLN B 544 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 696 ASN B 710 GLN B 740 ASN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 11686 Z= 0.250 Angle : 0.770 10.794 15832 Z= 0.407 Chirality : 0.045 0.173 1738 Planarity : 0.007 0.073 1944 Dihedral : 8.557 57.194 1560 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.92 % Allowed : 17.50 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.18), residues: 1344 helix: -2.28 (0.15), residues: 768 sheet: -5.01 (0.92), residues: 20 loop : -3.68 (0.20), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 397 HIS 0.003 0.001 HIS A 249 PHE 0.016 0.002 PHE A 685 TYR 0.026 0.002 TYR A 406 ARG 0.005 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 245 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.5577 (ttt180) cc_final: 0.5352 (ttp-170) REVERT: A 347 LEU cc_start: 0.6094 (tt) cc_final: 0.5317 (mp) REVERT: A 392 LEU cc_start: 0.8086 (mt) cc_final: 0.7749 (mt) REVERT: A 523 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8923 (mp) REVERT: A 618 ILE cc_start: 0.9087 (mm) cc_final: 0.8748 (mt) REVERT: A 659 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6406 (ptp) REVERT: A 700 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7686 (tt) REVERT: A 705 TRP cc_start: 0.7972 (t60) cc_final: 0.7677 (t60) REVERT: A 773 MET cc_start: 0.7225 (mmm) cc_final: 0.6566 (tpp) REVERT: B 305 TYR cc_start: 0.7663 (t80) cc_final: 0.7171 (t80) REVERT: B 700 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7958 (tt) REVERT: B 773 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.4604 (mtp) outliers start: 61 outliers final: 24 residues processed: 289 average time/residue: 0.2249 time to fit residues: 93.7531 Evaluate side-chains 240 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 866 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 0.0020 chunk 135 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN A 674 GLN A 696 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS B 129 HIS ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11686 Z= 0.192 Angle : 0.677 7.888 15832 Z= 0.357 Chirality : 0.043 0.146 1738 Planarity : 0.006 0.065 1944 Dihedral : 7.349 59.624 1533 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.52 % Allowed : 19.19 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.67 (0.19), residues: 1344 helix: -1.62 (0.17), residues: 776 sheet: None (None), residues: 0 loop : -3.64 (0.20), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 397 HIS 0.003 0.001 HIS A 275 PHE 0.027 0.001 PHE A 321 TYR 0.033 0.002 TYR A 242 ARG 0.007 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 224 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 LEU cc_start: 0.6377 (tt) cc_final: 0.5335 (mp) REVERT: A 392 LEU cc_start: 0.8090 (mt) cc_final: 0.7758 (mt) REVERT: A 534 MET cc_start: 0.7326 (mmt) cc_final: 0.6957 (mmt) REVERT: A 618 ILE cc_start: 0.8976 (mm) cc_final: 0.8672 (mt) REVERT: A 700 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7557 (tt) REVERT: A 705 TRP cc_start: 0.7864 (t60) cc_final: 0.7496 (t60) REVERT: A 742 MET cc_start: 0.7009 (mtt) cc_final: 0.6759 (mtp) REVERT: B 70 ARG cc_start: 0.7202 (ptm-80) cc_final: 0.6667 (ptt90) REVERT: B 305 TYR cc_start: 0.7606 (t80) cc_final: 0.7204 (t80) REVERT: B 700 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7940 (tt) outliers start: 56 outliers final: 34 residues processed: 261 average time/residue: 0.2228 time to fit residues: 84.2807 Evaluate side-chains 242 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 866 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11686 Z= 0.232 Angle : 0.680 8.113 15832 Z= 0.358 Chirality : 0.044 0.210 1738 Planarity : 0.006 0.060 1944 Dihedral : 6.903 59.109 1525 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 4.84 % Allowed : 20.48 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.29 (0.20), residues: 1344 helix: -1.27 (0.17), residues: 776 sheet: None (None), residues: 0 loop : -3.53 (0.20), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 397 HIS 0.004 0.001 HIS B 830 PHE 0.022 0.002 PHE A 321 TYR 0.038 0.002 TYR A 242 ARG 0.009 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 220 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8968 (mp) REVERT: A 534 MET cc_start: 0.7325 (mmt) cc_final: 0.6956 (mmt) REVERT: A 618 ILE cc_start: 0.9004 (mm) cc_final: 0.8689 (mt) REVERT: A 632 ASN cc_start: 0.7936 (m-40) cc_final: 0.7728 (m-40) REVERT: A 705 TRP cc_start: 0.7949 (t60) cc_final: 0.7610 (t60) REVERT: A 742 MET cc_start: 0.6945 (mtt) cc_final: 0.6668 (mtp) REVERT: B 305 TYR cc_start: 0.7688 (t80) cc_final: 0.7249 (t80) REVERT: B 591 TYR cc_start: 0.5644 (p90) cc_final: 0.5383 (t80) REVERT: B 659 MET cc_start: 0.6657 (ptm) cc_final: 0.6066 (ptt) REVERT: B 700 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7918 (tt) REVERT: B 839 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8069 (mm) outliers start: 60 outliers final: 33 residues processed: 259 average time/residue: 0.1997 time to fit residues: 76.7594 Evaluate side-chains 243 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 207 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 839 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11686 Z= 0.296 Angle : 0.726 11.422 15832 Z= 0.377 Chirality : 0.045 0.201 1738 Planarity : 0.006 0.059 1944 Dihedral : 6.864 59.810 1522 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 5.48 % Allowed : 21.37 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.20), residues: 1344 helix: -1.19 (0.17), residues: 792 sheet: None (None), residues: 0 loop : -3.43 (0.21), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 397 HIS 0.007 0.001 HIS A 818 PHE 0.023 0.002 PHE A 321 TYR 0.038 0.002 TYR A 242 ARG 0.008 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 219 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.3873 (tmt170) cc_final: 0.3284 (tmt170) REVERT: A 347 LEU cc_start: 0.6554 (tt) cc_final: 0.5624 (mp) REVERT: A 523 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8931 (mp) REVERT: A 534 MET cc_start: 0.7354 (mmt) cc_final: 0.7086 (mmt) REVERT: A 632 ASN cc_start: 0.7965 (m-40) cc_final: 0.7721 (m-40) REVERT: A 705 TRP cc_start: 0.8122 (t60) cc_final: 0.7740 (t60) REVERT: B 305 TYR cc_start: 0.7845 (t80) cc_final: 0.7352 (t80) REVERT: B 321 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6393 (p90) REVERT: B 700 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7928 (tt) outliers start: 68 outliers final: 49 residues processed: 264 average time/residue: 0.2116 time to fit residues: 83.3330 Evaluate side-chains 259 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 842 MET Chi-restraints excluded: chain B residue 843 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.0060 chunk 11 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.0040 chunk 128 optimal weight: 3.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11686 Z= 0.190 Angle : 0.665 9.185 15832 Z= 0.346 Chirality : 0.043 0.165 1738 Planarity : 0.006 0.059 1944 Dihedral : 6.630 59.318 1522 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.92 % Allowed : 22.26 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1344 helix: -0.96 (0.17), residues: 800 sheet: None (None), residues: 0 loop : -3.33 (0.23), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 397 HIS 0.003 0.001 HIS A 275 PHE 0.023 0.001 PHE A 321 TYR 0.033 0.001 TYR A 242 ARG 0.010 0.000 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 214 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 PRO cc_start: 0.7968 (Cg_exo) cc_final: 0.7587 (Cg_endo) REVERT: A 347 LEU cc_start: 0.6472 (tt) cc_final: 0.5459 (mp) REVERT: B 305 TYR cc_start: 0.7613 (t80) cc_final: 0.7221 (t80) REVERT: B 321 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6025 (p90) REVERT: B 631 MET cc_start: 0.7246 (mmm) cc_final: 0.7027 (mmm) REVERT: B 700 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7827 (tt) outliers start: 61 outliers final: 40 residues processed: 253 average time/residue: 0.2162 time to fit residues: 79.4482 Evaluate side-chains 244 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 202 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 768 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11686 Z= 0.323 Angle : 0.740 9.376 15832 Z= 0.386 Chirality : 0.047 0.187 1738 Planarity : 0.006 0.059 1944 Dihedral : 6.764 58.122 1522 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 4.84 % Allowed : 23.23 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.89 (0.21), residues: 1344 helix: -1.03 (0.17), residues: 794 sheet: None (None), residues: 0 loop : -3.27 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 397 HIS 0.007 0.001 HIS A 818 PHE 0.026 0.002 PHE A 321 TYR 0.027 0.002 TYR A 242 ARG 0.010 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 205 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 863 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.5938 (mp) REVERT: B 305 TYR cc_start: 0.7848 (t80) cc_final: 0.7350 (t80) REVERT: B 321 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6062 (p90) REVERT: B 523 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9022 (mp) REVERT: B 700 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7885 (tt) outliers start: 60 outliers final: 43 residues processed: 245 average time/residue: 0.2017 time to fit residues: 73.0042 Evaluate side-chains 245 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 198 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.0470 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11686 Z= 0.204 Angle : 0.676 10.147 15832 Z= 0.352 Chirality : 0.044 0.171 1738 Planarity : 0.006 0.060 1944 Dihedral : 6.202 58.750 1520 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.87 % Allowed : 24.27 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.21), residues: 1344 helix: -0.77 (0.17), residues: 796 sheet: None (None), residues: 0 loop : -3.24 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 397 HIS 0.004 0.001 HIS A 844 PHE 0.027 0.001 PHE A 321 TYR 0.027 0.001 TYR A 242 ARG 0.009 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 MET cc_start: 0.7993 (mmm) cc_final: 0.7790 (mmm) REVERT: B 305 TYR cc_start: 0.7679 (t80) cc_final: 0.7286 (t80) REVERT: B 321 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.5584 (p90) REVERT: B 523 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8976 (mp) REVERT: B 700 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7860 (tt) outliers start: 48 outliers final: 38 residues processed: 239 average time/residue: 0.2225 time to fit residues: 77.2451 Evaluate side-chains 240 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 0.0980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11686 Z= 0.214 Angle : 0.681 11.303 15832 Z= 0.353 Chirality : 0.044 0.190 1738 Planarity : 0.006 0.060 1944 Dihedral : 6.116 58.006 1520 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.19 % Allowed : 23.95 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1344 helix: -0.68 (0.18), residues: 798 sheet: None (None), residues: 0 loop : -3.19 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 389 HIS 0.005 0.001 HIS B 844 PHE 0.031 0.002 PHE A 321 TYR 0.023 0.001 TYR A 242 ARG 0.008 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 210 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.7619 (t80) cc_final: 0.7400 (t80) REVERT: A 321 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.6400 (p90) REVERT: A 542 ARG cc_start: 0.6588 (ttp80) cc_final: 0.6358 (ttp80) REVERT: A 555 MET cc_start: 0.7616 (tpt) cc_final: 0.7257 (tpt) REVERT: B 305 TYR cc_start: 0.7726 (t80) cc_final: 0.7317 (t80) REVERT: B 321 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.5631 (p90) REVERT: B 523 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8975 (mp) REVERT: B 534 MET cc_start: 0.7898 (mpp) cc_final: 0.7535 (mmt) REVERT: B 700 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7838 (tt) outliers start: 52 outliers final: 40 residues processed: 241 average time/residue: 0.2270 time to fit residues: 80.3316 Evaluate side-chains 245 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 201 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 91 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 67 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11686 Z= 0.188 Angle : 0.669 12.067 15832 Z= 0.345 Chirality : 0.044 0.202 1738 Planarity : 0.006 0.061 1944 Dihedral : 6.009 57.553 1520 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.63 % Allowed : 24.19 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.21), residues: 1344 helix: -0.49 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -3.14 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 389 HIS 0.005 0.001 HIS A 275 PHE 0.029 0.001 PHE A 321 TYR 0.020 0.001 TYR A 242 ARG 0.008 0.000 ARG B 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.6570 (tptp) cc_final: 0.6346 (mtmm) REVERT: A 70 ARG cc_start: 0.7324 (ptm-80) cc_final: 0.7063 (ptm-80) REVERT: A 321 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.6086 (p90) REVERT: A 555 MET cc_start: 0.7697 (tpt) cc_final: 0.7291 (tpt) REVERT: A 705 TRP cc_start: 0.7685 (t60) cc_final: 0.7446 (t60) REVERT: B 305 TYR cc_start: 0.7641 (t80) cc_final: 0.7265 (t80) REVERT: B 321 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.5507 (p90) REVERT: B 523 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8946 (mp) REVERT: B 629 TRP cc_start: 0.6924 (t60) cc_final: 0.5937 (t60) REVERT: B 700 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7792 (tt) outliers start: 45 outliers final: 35 residues processed: 237 average time/residue: 0.2160 time to fit residues: 74.0373 Evaluate side-chains 242 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 573 PHE Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.232743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.195080 restraints weight = 15320.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.195202 restraints weight = 12973.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.197172 restraints weight = 11462.626| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11686 Z= 0.321 Angle : 0.753 12.187 15832 Z= 0.392 Chirality : 0.047 0.210 1738 Planarity : 0.006 0.061 1944 Dihedral : 6.297 59.833 1520 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.03 % Allowed : 24.11 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.21), residues: 1344 helix: -0.69 (0.17), residues: 796 sheet: None (None), residues: 0 loop : -3.06 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 397 HIS 0.006 0.002 HIS B 818 PHE 0.032 0.002 PHE A 321 TYR 0.045 0.002 TYR B 477 ARG 0.019 0.001 ARG B 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2340.68 seconds wall clock time: 43 minutes 3.44 seconds (2583.44 seconds total)