Starting phenix.real_space_refine on Mon Mar 18 02:36:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta5_41129/03_2024/8ta5_41129.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta5_41129/03_2024/8ta5_41129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta5_41129/03_2024/8ta5_41129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta5_41129/03_2024/8ta5_41129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta5_41129/03_2024/8ta5_41129.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta5_41129/03_2024/8ta5_41129.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.155 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: 6 Type Number sf(0) Gaussians S 56 5.16 5 Cl 2 4.86 5 C 6376 2.51 5 N 1634 2.21 5 O 1666 1.98 5 H 10041 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 235": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 558": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 586": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 598": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 601": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 610": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 629": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 644": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 800": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 825": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 836": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 235": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 558": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 577": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 579": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 586": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 598": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 601": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 606": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 610": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 629": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 644": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 800": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 825": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 836": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19775 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 9886 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 28, 'TRANS': 596} Chain breaks: 4 Chain: "B" Number of atoms: 9887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 9887 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 28, 'TRANS': 596} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.71, per 1000 atoms: 0.44 Number of scatterers: 19775 At special positions: 0 Unit cell: (118.25, 77.572, 117.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 56 16.00 O 1666 8.00 N 1634 7.00 C 6376 6.00 H 10041 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.60 Conformation dependent library (CDL) restraints added in 2.1 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 67.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 89 through 124 Processing helix chain 'A' and resid 129 through 156 removed outlier: 3.770A pdb=" N TYR A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.589A pdb=" N VAL A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.510A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.913A pdb=" N MET A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.627A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 364 through 378 removed outlier: 3.525A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 388 removed outlier: 4.106A pdb=" N GLN A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 388 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 420 through 425 removed outlier: 4.274A pdb=" N TRP A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 450 removed outlier: 3.914A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 removed outlier: 3.558A pdb=" N VAL A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.951A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 Processing helix chain 'A' and resid 530 through 547 removed outlier: 3.680A pdb=" N SER A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.384A pdb=" N GLN A 575 " --> pdb=" O ARG A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.687A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.701A pdb=" N LEU A 602 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 641 removed outlier: 4.018A pdb=" N ALA A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 779 removed outlier: 4.303A pdb=" N LEU A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 779' Processing helix chain 'A' and resid 802 through 813 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'B' and resid 89 through 126 removed outlier: 3.584A pdb=" N PHE B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.543A pdb=" N VAL B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 204 through 223 Processing helix chain 'B' and resid 231 through 253 removed outlier: 5.256A pdb=" N ALA B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 272 through 294 removed outlier: 3.599A pdb=" N VAL B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 removed outlier: 3.585A pdb=" N VAL B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 364 through 378 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.654A pdb=" N ALA B 388 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 430 through 450 removed outlier: 3.965A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 removed outlier: 3.562A pdb=" N VAL B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.834A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 530 through 547 removed outlier: 3.527A pdb=" N SER B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.543A pdb=" N ARG B 577 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 584 removed outlier: 3.849A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 606 Processing helix chain 'B' and resid 629 through 641 Processing helix chain 'B' and resid 802 through 813 Processing helix chain 'B' and resid 832 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.881A pdb=" N PHE A 270 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 270 " --> pdb=" O PHE A 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 592 removed outlier: 6.491A pdb=" N LEU A 612 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER A 626 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 614 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 817 through 821 removed outlier: 3.566A pdb=" N GLY A 828 " --> pdb=" O VAL A 820 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 Processing sheet with id=AA6, first strand: chain 'B' and resid 590 through 592 removed outlier: 6.520A pdb=" N VAL B 591 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 612 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 626 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 614 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 817 through 822 removed outlier: 6.351A pdb=" N SER B 822 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1764 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: 7.06 Time building geometry restraints manager: 16.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 10023 1.13 - 1.30: 1618 1.30 - 1.48: 3888 1.48 - 1.65: 4378 1.65 - 1.82: 94 Bond restraints: 20001 Sorted by residual: bond pdb=" N HIS A 804 " pdb=" H HIS A 804 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR A 450 " pdb=" H THR A 450 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ARG B 610 " pdb=" H ARG B 610 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N PHE A 261 " pdb=" H PHE A 261 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD1 PHE B 383 " pdb=" HD1 PHE B 383 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 19996 not shown) Histogram of bond angle deviations from ideal: 96.46 - 104.14: 176 104.14 - 111.82: 21412 111.82 - 119.50: 7571 119.50 - 127.19: 6918 127.19 - 134.87: 139 Bond angle restraints: 36216 Sorted by residual: angle pdb=" CA ASP A 402 " pdb=" CB ASP A 402 " pdb=" CG ASP A 402 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" CA ASP B 791 " pdb=" CB ASP B 791 " pdb=" CG ASP B 791 " ideal model delta sigma weight residual 112.60 118.16 -5.56 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA ASP B 313 " pdb=" CB ASP B 313 " pdb=" CG ASP B 313 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" CA ASP B 402 " pdb=" CB ASP B 402 " pdb=" CG ASP B 402 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA PHE B 401 " pdb=" CB PHE B 401 " pdb=" CG PHE B 401 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 ... (remaining 36211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 8512 17.73 - 35.47: 454 35.47 - 53.20: 160 53.20 - 70.93: 231 70.93 - 88.66: 18 Dihedral angle restraints: 9375 sinusoidal: 5044 harmonic: 4331 Sorted by residual: dihedral pdb=" CA GLY B 161 " pdb=" C GLY B 161 " pdb=" N SER B 162 " pdb=" CA SER B 162 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU B 176 " pdb=" C LEU B 176 " pdb=" N LYS B 177 " pdb=" CA LYS B 177 " ideal model delta harmonic sigma weight residual 180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP A 317 " pdb=" C ASP A 317 " pdb=" N LEU A 318 " pdb=" CA LEU A 318 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1000 0.078 - 0.155: 446 0.155 - 0.233: 122 0.233 - 0.310: 13 0.310 - 0.388: 5 Chirality restraints: 1586 Sorted by residual: chirality pdb=" CA PRO A 380 " pdb=" N PRO A 380 " pdb=" C PRO A 380 " pdb=" CB PRO A 380 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA PRO B 380 " pdb=" N PRO B 380 " pdb=" C PRO B 380 " pdb=" CB PRO B 380 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ASP B 402 " pdb=" N ASP B 402 " pdb=" C ASP B 402 " pdb=" CB ASP B 402 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1583 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 404 " 0.196 9.50e-02 1.11e+02 1.53e-01 4.32e+02 pdb=" NE ARG B 404 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 404 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 404 " -0.073 2.00e-02 2.50e+03 pdb=" NH2 ARG B 404 " 0.033 2.00e-02 2.50e+03 pdb="HH11 ARG B 404 " -0.177 2.00e-02 2.50e+03 pdb="HH12 ARG B 404 " 0.293 2.00e-02 2.50e+03 pdb="HH21 ARG B 404 " 0.056 2.00e-02 2.50e+03 pdb="HH22 ARG B 404 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 25 " 0.275 9.50e-02 1.11e+02 1.21e-01 1.46e+02 pdb=" NE ARG B 25 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG B 25 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG B 25 " 0.093 2.00e-02 2.50e+03 pdb=" NH2 ARG B 25 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 25 " -0.178 2.00e-02 2.50e+03 pdb="HH12 ARG B 25 " 0.068 2.00e-02 2.50e+03 pdb="HH21 ARG B 25 " -0.072 2.00e-02 2.50e+03 pdb="HH22 ARG B 25 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.142 2.00e-02 2.50e+03 5.11e-02 1.05e+02 pdb=" CG TRP A 106 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 TRP A 106 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP A 106 " 0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP A 106 " 0.073 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 106 " -0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 106 " -0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP A 106 " -0.069 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 914 2.18 - 2.79: 34141 2.79 - 3.39: 55064 3.39 - 4.00: 75504 4.00 - 4.60: 106702 Nonbonded interactions: 272325 Sorted by model distance: nonbonded pdb=" OE2 GLU B 264 " pdb=" HG SER B 516 " model vdw 1.580 1.850 nonbonded pdb=" OE2 GLU A 264 " pdb=" HG SER A 516 " model vdw 1.581 1.850 nonbonded pdb=" OE1 GLU B 320 " pdb=" HH TYR B 499 " model vdw 1.600 1.850 nonbonded pdb=" OE1 GLU A 238 " pdb=" HH TYR B 576 " model vdw 1.605 1.850 nonbonded pdb=" HG1 THR A 831 " pdb=" OE1 GLU A 834 " model vdw 1.607 1.850 ... (remaining 272320 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' and (resid 14 through 512 or (resid 513 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 514 through 841 or resid 901)) } 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 individual isotropic 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: 0.690 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: 0.280 Extract box with map and model: 4.690 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 62.530 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 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 : 0.013 0.041 9960 Z= 0.827 Angle : 1.801 8.204 13530 Z= 1.242 Chirality : 0.091 0.388 1586 Planarity : 0.013 0.134 1676 Dihedral : 13.219 88.665 3536 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 1.36 % Allowed : 2.62 % Favored : 96.03 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.20), residues: 1230 helix: -0.54 (0.15), residues: 776 sheet: -1.52 (1.16), residues: 20 loop : -0.93 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.013 TRP A 106 HIS 0.009 0.003 HIS A 513 PHE 0.064 0.012 PHE A 270 TYR 0.066 0.012 TYR A 23 ARG 0.008 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8420 (tptp) cc_final: 0.8163 (tppt) REVERT: B 450 THR cc_start: 0.7582 (m) cc_final: 0.7254 (p) outliers start: 14 outliers final: 4 residues processed: 169 average time/residue: 2.2759 time to fit residues: 417.0633 Evaluate side-chains 108 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 425 ASN A 796 GLN B 542 ASN B 549 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9960 Z= 0.277 Angle : 0.653 5.913 13530 Z= 0.359 Chirality : 0.041 0.135 1586 Planarity : 0.005 0.049 1676 Dihedral : 5.450 41.048 1348 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.23 % Allowed : 6.59 % Favored : 91.18 % 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: 0.50 (0.22), residues: 1230 helix: 1.28 (0.17), residues: 780 sheet: -1.50 (0.71), residues: 38 loop : -1.32 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 295 HIS 0.008 0.002 HIS A 513 PHE 0.015 0.002 PHE B 459 TYR 0.011 0.001 TYR A 140 ARG 0.005 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8440 (tptp) cc_final: 0.8064 (tppt) REVERT: A 460 MET cc_start: 0.7805 (mmt) cc_final: 0.7477 (mmt) REVERT: A 816 ASP cc_start: 0.6034 (t0) cc_final: 0.5634 (t0) REVERT: B 101 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8122 (tpt) REVERT: B 266 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7295 (t) REVERT: B 450 THR cc_start: 0.7718 (m) cc_final: 0.7362 (p) REVERT: B 460 MET cc_start: 0.8272 (mmm) cc_final: 0.7939 (mmt) REVERT: B 538 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8089 (t) outliers start: 23 outliers final: 13 residues processed: 129 average time/residue: 1.9197 time to fit residues: 273.4054 Evaluate side-chains 111 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN A 425 ASN B 530 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9960 Z= 0.316 Angle : 0.709 17.896 13530 Z= 0.383 Chirality : 0.043 0.152 1586 Planarity : 0.006 0.052 1676 Dihedral : 5.200 43.884 1344 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.84 % Allowed : 8.43 % Favored : 89.73 % 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: 0.43 (0.23), residues: 1230 helix: 1.33 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 295 HIS 0.009 0.002 HIS B 530 PHE 0.020 0.003 PHE B 279 TYR 0.016 0.002 TYR B 275 ARG 0.024 0.001 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.8004 (mmt) cc_final: 0.7639 (mmt) REVERT: B 238 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6350 (mt-10) REVERT: B 386 PHE cc_start: 0.8027 (m-80) cc_final: 0.7600 (m-80) REVERT: B 450 THR cc_start: 0.8595 (m) cc_final: 0.8192 (p) REVERT: B 460 MET cc_start: 0.8383 (mmm) cc_final: 0.8095 (mmt) REVERT: B 480 TRP cc_start: 0.6771 (t-100) cc_final: 0.5788 (t60) outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 2.1487 time to fit residues: 288.7094 Evaluate side-chains 104 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9960 Z= 0.226 Angle : 0.543 6.384 13530 Z= 0.291 Chirality : 0.039 0.165 1586 Planarity : 0.005 0.046 1676 Dihedral : 4.813 42.806 1344 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 9.11 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1230 helix: 1.95 (0.18), residues: 788 sheet: -0.53 (1.14), residues: 18 loop : -1.55 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 295 HIS 0.005 0.001 HIS B 573 PHE 0.019 0.001 PHE A 226 TYR 0.009 0.001 TYR B 492 ARG 0.003 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8678 (tptp) cc_final: 0.8305 (tppt) REVERT: A 387 MET cc_start: 0.8615 (ptm) cc_final: 0.8365 (ptm) REVERT: A 404 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7273 (mtm110) REVERT: B 349 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6729 (mtm) REVERT: B 450 THR cc_start: 0.8533 (m) cc_final: 0.8082 (p) REVERT: B 460 MET cc_start: 0.8339 (mmm) cc_final: 0.8101 (mmt) REVERT: B 480 TRP cc_start: 0.6990 (t-100) cc_final: 0.5854 (t60) REVERT: B 584 MET cc_start: 0.1439 (mmt) cc_final: 0.0384 (mmt) outliers start: 21 outliers final: 13 residues processed: 113 average time/residue: 1.9316 time to fit residues: 241.5852 Evaluate side-chains 105 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 HIS A 807 HIS B 486 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9960 Z= 0.260 Angle : 0.556 6.907 13530 Z= 0.300 Chirality : 0.040 0.144 1586 Planarity : 0.005 0.047 1676 Dihedral : 4.699 44.199 1344 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.42 % Allowed : 10.08 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1230 helix: 2.00 (0.18), residues: 788 sheet: -1.04 (1.01), residues: 18 loop : -1.64 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 121 HIS 0.005 0.002 HIS A 804 PHE 0.013 0.002 PHE B 379 TYR 0.011 0.002 TYR A 819 ARG 0.005 0.001 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8646 (tptp) cc_final: 0.8279 (tppt) REVERT: A 404 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7458 (mtm180) REVERT: A 820 VAL cc_start: -0.1107 (OUTLIER) cc_final: -0.1630 (t) REVERT: B 221 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7161 (ttpp) REVERT: B 365 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8184 (tp) REVERT: B 450 THR cc_start: 0.8549 (m) cc_final: 0.8076 (p) REVERT: B 460 MET cc_start: 0.8382 (mmm) cc_final: 0.8141 (mmt) REVERT: B 584 MET cc_start: 0.1286 (mmt) cc_final: -0.0353 (mmt) outliers start: 25 outliers final: 15 residues processed: 120 average time/residue: 2.1072 time to fit residues: 277.1900 Evaluate side-chains 112 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.0370 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9960 Z= 0.161 Angle : 0.482 5.146 13530 Z= 0.259 Chirality : 0.037 0.181 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.478 42.672 1344 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.65 % Allowed : 11.53 % Favored : 86.82 % 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: 1.56 (0.24), residues: 1230 helix: 2.36 (0.18), residues: 786 sheet: -1.24 (1.01), residues: 18 loop : -1.51 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 295 HIS 0.003 0.001 HIS A 804 PHE 0.011 0.001 PHE B 314 TYR 0.007 0.001 TYR A 819 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ASP cc_start: 0.8377 (p0) cc_final: 0.7985 (p0) REVERT: A 404 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7446 (mtm110) REVERT: A 430 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7431 (m-40) REVERT: B 221 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7152 (ttpp) REVERT: B 450 THR cc_start: 0.8560 (m) cc_final: 0.8108 (p) REVERT: B 584 MET cc_start: 0.1376 (mmt) cc_final: -0.0116 (mmt) outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 2.1387 time to fit residues: 253.1347 Evaluate side-chains 104 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9960 Z= 0.174 Angle : 0.474 5.101 13530 Z= 0.254 Chirality : 0.037 0.131 1586 Planarity : 0.004 0.044 1676 Dihedral : 4.325 41.861 1344 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.45 % Allowed : 12.31 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1230 helix: 2.51 (0.18), residues: 788 sheet: -1.32 (1.03), residues: 18 loop : -1.48 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.003 0.001 HIS B 573 PHE 0.012 0.001 PHE A 279 TYR 0.009 0.001 TYR B 275 ARG 0.003 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.530 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 344 LYS cc_start: 0.8627 (tptp) cc_final: 0.8251 (tppt) REVERT: A 387 MET cc_start: 0.8614 (ptm) cc_final: 0.8378 (ptm) REVERT: A 402 ASP cc_start: 0.8392 (p0) cc_final: 0.8006 (p0) REVERT: A 404 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7426 (mtm180) REVERT: A 430 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7491 (m-40) REVERT: A 483 ASP cc_start: 0.8067 (m-30) cc_final: 0.7819 (m-30) REVERT: A 816 ASP cc_start: 0.7416 (t0) cc_final: 0.6913 (p0) REVERT: B 450 THR cc_start: 0.8560 (m) cc_final: 0.8097 (p) REVERT: B 584 MET cc_start: 0.1378 (mmt) cc_final: -0.0312 (mmt) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 2.0780 time to fit residues: 248.4329 Evaluate side-chains 101 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9960 Z= 0.150 Angle : 0.465 5.017 13530 Z= 0.249 Chirality : 0.037 0.216 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.101 28.410 1342 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.55 % Allowed : 12.02 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.24), residues: 1230 helix: 2.67 (0.18), residues: 786 sheet: -1.15 (1.06), residues: 18 loop : -1.40 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 295 HIS 0.002 0.001 HIS A 807 PHE 0.008 0.001 PHE A 379 TYR 0.006 0.001 TYR B 275 ARG 0.003 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.8576 (ptm) cc_final: 0.8318 (ptm) REVERT: A 402 ASP cc_start: 0.8298 (p0) cc_final: 0.7980 (p0) REVERT: A 404 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7426 (mtm180) REVERT: A 816 ASP cc_start: 0.7478 (t0) cc_final: 0.7011 (p0) REVERT: B 221 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7013 (ttpp) REVERT: B 425 ASN cc_start: 0.7787 (p0) cc_final: 0.7372 (t0) REVERT: B 584 MET cc_start: 0.1378 (mmt) cc_final: -0.0195 (mmt) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 2.1778 time to fit residues: 257.4485 Evaluate side-chains 102 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.7474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9960 Z= 0.238 Angle : 0.512 5.153 13530 Z= 0.276 Chirality : 0.039 0.160 1586 Planarity : 0.005 0.044 1676 Dihedral : 4.225 27.607 1342 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.74 % Allowed : 12.11 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1230 helix: 2.44 (0.18), residues: 788 sheet: -1.04 (1.08), residues: 18 loop : -1.53 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 121 HIS 0.004 0.001 HIS A 804 PHE 0.011 0.001 PHE B 379 TYR 0.011 0.001 TYR B 275 ARG 0.004 0.000 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7159 (t60) cc_final: 0.6825 (t60) REVERT: A 402 ASP cc_start: 0.8515 (p0) cc_final: 0.8107 (p0) REVERT: A 404 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7607 (mtm180) REVERT: A 408 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.5758 (ptt-90) REVERT: A 430 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7691 (m-40) REVERT: A 816 ASP cc_start: 0.7635 (t0) cc_final: 0.7290 (p0) REVERT: B 221 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7043 (ttpp) REVERT: B 312 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7844 (mt) REVERT: B 425 ASN cc_start: 0.7765 (p0) cc_final: 0.7499 (t0) REVERT: B 483 ASP cc_start: 0.7837 (t0) cc_final: 0.7174 (p0) REVERT: B 584 MET cc_start: 0.1254 (mmt) cc_final: -0.0282 (mmt) outliers start: 18 outliers final: 10 residues processed: 119 average time/residue: 2.0759 time to fit residues: 271.4423 Evaluate side-chains 114 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9960 Z= 0.160 Angle : 0.472 5.040 13530 Z= 0.253 Chirality : 0.037 0.192 1586 Planarity : 0.004 0.042 1676 Dihedral : 4.084 27.697 1342 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.36 % Allowed : 12.60 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.24), residues: 1230 helix: 2.66 (0.18), residues: 784 sheet: -1.02 (1.10), residues: 18 loop : -1.50 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 121 HIS 0.002 0.001 HIS B 807 PHE 0.015 0.001 PHE A 279 TYR 0.007 0.001 TYR B 275 ARG 0.002 0.000 ARG A 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7263 (t60) cc_final: 0.6863 (t60) REVERT: A 402 ASP cc_start: 0.8466 (p0) cc_final: 0.8053 (p0) REVERT: A 404 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7467 (mtm180) REVERT: A 816 ASP cc_start: 0.7635 (t0) cc_final: 0.7299 (p0) REVERT: B 221 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7045 (ttpp) REVERT: B 483 ASP cc_start: 0.7792 (t0) cc_final: 0.7158 (p0) REVERT: B 584 MET cc_start: 0.1273 (mmt) cc_final: -0.0151 (mmt) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 2.0047 time to fit residues: 244.9584 Evaluate side-chains 110 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 546 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.202573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142537 restraints weight = 31723.849| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.29 r_work: 0.3591 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.7731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9960 Z= 0.171 Angle : 0.470 5.064 13530 Z= 0.252 Chirality : 0.037 0.175 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.014 27.710 1342 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.45 % Allowed : 12.60 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.24), residues: 1230 helix: 2.71 (0.18), residues: 784 sheet: -1.11 (1.11), residues: 18 loop : -1.51 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.004 0.001 HIS A 807 PHE 0.014 0.001 PHE A 279 TYR 0.008 0.001 TYR B 275 ARG 0.003 0.000 ARG A 800 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6176.99 seconds wall clock time: 108 minutes 31.37 seconds (6511.37 seconds total)