Starting phenix.real_space_refine on Sat Jul 20 20:15:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/07_2024/8rfh_19121.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/07_2024/8rfh_19121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/07_2024/8rfh_19121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/07_2024/8rfh_19121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/07_2024/8rfh_19121.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/07_2024/8rfh_19121.cif" } resolution = 3.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic. 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 P 4 5.49 5 S 58 5.16 5 C 7550 2.51 5 N 2032 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B GLU 610": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11802 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5874 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696} Chain breaks: 1 Chain: "B" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5874 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.72, per 1000 atoms: 0.57 Number of scatterers: 11802 At special positions: 0 Unit cell: (141.588, 78.66, 91.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 4 15.00 O 2158 8.00 N 2032 7.00 C 7550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.0 seconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 12 sheets defined 43.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.575A pdb=" N LYS A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.662A pdb=" N HIS A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.559A pdb=" N GLY A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.520A pdb=" N TRP A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 4.287A pdb=" N ALA A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.550A pdb=" N ILE A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 4.111A pdb=" N LEU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.763A pdb=" N ASN A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.688A pdb=" N GLY A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 445 through 460 Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 526 through 534 removed outlier: 3.534A pdb=" N LYS A 534 " --> pdb=" O PHE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 679 through 685 Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.862A pdb=" N LEU A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.878A pdb=" N VAL A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 757 through 759 No H-bonds generated for 'chain 'A' and resid 757 through 759' Processing helix chain 'A' and resid 760 through 767 removed outlier: 3.640A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 838 Processing helix chain 'A' and resid 850 through 871 Processing helix chain 'B' and resid 157 through 170 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 218 through 229 removed outlier: 3.575A pdb=" N LYS B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.661A pdb=" N HIS B 238 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 256 removed outlier: 3.559A pdb=" N GLY B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.520A pdb=" N TRP B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 4.288A pdb=" N ALA B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 334 through 348 removed outlier: 4.111A pdb=" N LEU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.763A pdb=" N ASN B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 415 removed outlier: 3.687A pdb=" N GLY B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 445 through 460 Processing helix chain 'B' and resid 480 through 494 Processing helix chain 'B' and resid 511 through 516 Processing helix chain 'B' and resid 526 through 534 removed outlier: 3.533A pdb=" N LYS B 534 " --> pdb=" O PHE B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 605 through 611 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 685 Processing helix chain 'B' and resid 697 through 702 removed outlier: 3.861A pdb=" N LEU B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.879A pdb=" N VAL B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 760 through 767 removed outlier: 3.640A pdb=" N LEU B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 767 " --> pdb=" O ILE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 850 through 871 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 212 removed outlier: 3.567A pdb=" N ILE A 209 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 265 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU A 176 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 290 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL A 178 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 292 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL A 180 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.609A pdb=" N GLN A 467 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG A 478 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL A 465 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.818A pdb=" N PHE A 543 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 574 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.818A pdb=" N PHE A 543 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 574 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N TYR A 593 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N GLU A 574 " --> pdb=" O TYR A 593 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ALA A 595 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 576 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 594 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASN A 620 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 596 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 641 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE A 673 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N THR A 643 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A 669 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY A 693 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER A 671 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG A 695 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE A 673 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 752 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 725 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 749 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS A 776 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 751 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 845 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 822 " --> pdb=" O GLU A 845 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 604 Processing sheet with id=AA6, first strand: chain 'A' and resid 784 through 786 removed outlier: 6.691A pdb=" N TRP A 785 " --> pdb=" O LYS A 808 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 207 through 212 removed outlier: 3.567A pdb=" N ILE B 209 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 265 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU B 176 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU B 290 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 178 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR B 292 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL B 180 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 423 through 424 removed outlier: 3.608A pdb=" N GLN B 467 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG B 478 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL B 465 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.819A pdb=" N PHE B 543 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLU B 574 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.819A pdb=" N PHE B 543 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLU B 574 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TYR B 593 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N GLU B 574 " --> pdb=" O TYR B 593 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ALA B 595 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 576 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 594 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ASN B 620 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 596 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 641 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE B 673 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N THR B 643 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 672 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ARG B 695 " --> pdb=" O THR B 672 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 752 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 725 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 749 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS B 776 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B 751 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 845 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 822 " --> pdb=" O GLU B 845 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 603 through 604 Processing sheet with id=AB3, first strand: chain 'B' and resid 784 through 786 removed outlier: 6.690A pdb=" N TRP B 785 " --> pdb=" O LYS B 808 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 458 hydrogen bonds defined for protein. 1254 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: 4.13 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3588 1.34 - 1.45: 1609 1.45 - 1.57: 6771 1.57 - 1.69: 6 1.69 - 1.81: 82 Bond restraints: 12056 Sorted by residual: bond pdb=" N THR A 315 " pdb=" CA THR A 315 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.31e-02 5.83e+03 1.08e+01 bond pdb=" N ILE A 673 " pdb=" CA ILE A 673 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N THR B 315 " pdb=" CA THR B 315 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.34e-02 5.57e+03 9.89e+00 bond pdb=" N LEU A 314 " pdb=" CA LEU A 314 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.79e+00 bond pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.15e+00 ... (remaining 12051 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.52: 210 105.52 - 113.12: 6681 113.12 - 120.73: 5335 120.73 - 128.33: 3961 128.33 - 135.93: 99 Bond angle restraints: 16286 Sorted by residual: angle pdb=" C SER A 671 " pdb=" N THR A 672 " pdb=" CA THR A 672 " ideal model delta sigma weight residual 122.30 114.12 8.18 1.35e+00 5.49e-01 3.67e+01 angle pdb=" C THR A 672 " pdb=" CA THR A 672 " pdb=" CB THR A 672 " ideal model delta sigma weight residual 110.22 120.17 -9.95 1.67e+00 3.59e-01 3.55e+01 angle pdb=" N ASP B 317 " pdb=" CA ASP B 317 " pdb=" C ASP B 317 " ideal model delta sigma weight residual 111.28 105.88 5.40 1.09e+00 8.42e-01 2.46e+01 angle pdb=" N ASP A 317 " pdb=" CA ASP A 317 " pdb=" C ASP A 317 " ideal model delta sigma weight residual 111.28 106.71 4.57 1.09e+00 8.42e-01 1.76e+01 angle pdb=" C GLU A 316 " pdb=" CA GLU A 316 " pdb=" CB GLU A 316 " ideal model delta sigma weight residual 110.79 105.33 5.46 1.66e+00 3.63e-01 1.08e+01 ... (remaining 16281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 7135 34.69 - 69.38: 185 69.38 - 104.07: 12 104.07 - 138.76: 0 138.76 - 173.45: 2 Dihedral angle restraints: 7334 sinusoidal: 3096 harmonic: 4238 Sorted by residual: dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 113.45 -173.45 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 113.42 -173.42 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA SER A 671 " pdb=" C SER A 671 " pdb=" N THR A 672 " pdb=" CA THR A 672 " ideal model delta harmonic sigma weight residual -180.00 -150.32 -29.68 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 7331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1622 0.078 - 0.156: 182 0.156 - 0.234: 7 0.234 - 0.311: 0 0.311 - 0.389: 1 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA THR A 672 " pdb=" N THR A 672 " pdb=" C THR A 672 " pdb=" CB THR A 672 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA GLU A 316 " pdb=" N GLU A 316 " pdb=" C GLU A 316 " pdb=" CB GLU A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B 673 " pdb=" N ILE B 673 " pdb=" C ILE B 673 " pdb=" CB ILE B 673 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1809 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 670 " 0.021 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C LEU A 670 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU A 670 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 671 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 670 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C LEU B 670 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 670 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 671 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 671 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C SER A 671 " -0.048 2.00e-02 2.50e+03 pdb=" O SER A 671 " 0.018 2.00e-02 2.50e+03 pdb=" N THR A 672 " 0.016 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 859 2.74 - 3.28: 12589 3.28 - 3.82: 20182 3.82 - 4.36: 23810 4.36 - 4.90: 38512 Nonbonded interactions: 95952 Sorted by model distance: nonbonded pdb=" OG1 THR B 469 " pdb=" OD1 ASP B 471 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR A 469 " pdb=" OD1 ASP A 471 " model vdw 2.201 2.440 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASP A 270 " model vdw 2.280 2.440 nonbonded pdb=" OG SER B 268 " pdb=" OD1 ASP B 270 " model vdw 2.280 2.440 nonbonded pdb=" O VAL A 653 " pdb=" NH2 ARG A 685 " model vdw 2.293 2.520 ... (remaining 95947 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.110 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.003 0.043 12056 Z= 0.203 Angle : 0.760 11.116 16286 Z= 0.383 Chirality : 0.048 0.389 1812 Planarity : 0.004 0.043 2060 Dihedral : 15.836 173.446 4582 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.69 % Favored : 97.18 % Rotamer: Outliers : 1.44 % Allowed : 21.35 % Favored : 77.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.03 % 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: 0.66 (0.23), residues: 1452 helix: 0.50 (0.23), residues: 518 sheet: 0.20 (0.37), residues: 212 loop : 0.67 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 798 HIS 0.004 0.001 HIS A 524 PHE 0.010 0.001 PHE B 571 TYR 0.006 0.001 TYR B 413 ARG 0.007 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.403 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 351 LEU cc_start: 0.7900 (tt) cc_final: 0.7248 (tp) REVERT: A 456 ASP cc_start: 0.8905 (m-30) cc_final: 0.8319 (t70) REVERT: A 692 LEU cc_start: 0.9270 (tp) cc_final: 0.9021 (tp) REVERT: A 844 MET cc_start: 0.7277 (tmm) cc_final: 0.7032 (tmm) REVERT: B 351 LEU cc_start: 0.7779 (tt) cc_final: 0.7215 (tp) REVERT: B 432 TRP cc_start: 0.8378 (m-10) cc_final: 0.8029 (m-90) REVERT: B 456 ASP cc_start: 0.8881 (m-30) cc_final: 0.8274 (t70) REVERT: B 671 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6842 (p) REVERT: B 672 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6154 (p) REVERT: B 692 LEU cc_start: 0.9234 (tp) cc_final: 0.9018 (tp) REVERT: B 844 MET cc_start: 0.7143 (tmm) cc_final: 0.6898 (tmm) outliers start: 19 outliers final: 3 residues processed: 194 average time/residue: 0.2023 time to fit residues: 59.2336 Evaluate side-chains 172 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 672 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 40.0000 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 132 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN B 309 HIS B 349 ASN B 668 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12056 Z= 0.164 Angle : 0.657 10.320 16286 Z= 0.309 Chirality : 0.044 0.149 1812 Planarity : 0.004 0.043 2060 Dihedral : 7.210 145.140 1586 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.12 % Allowed : 17.63 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.38 (0.22), residues: 1452 helix: 0.56 (0.23), residues: 544 sheet: -0.02 (0.37), residues: 200 loop : 0.27 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 432 HIS 0.004 0.001 HIS A 524 PHE 0.017 0.001 PHE A 585 TYR 0.013 0.001 TYR A 259 ARG 0.005 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 1.497 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 407 LEU cc_start: 0.9499 (tp) cc_final: 0.9081 (tp) REVERT: A 456 ASP cc_start: 0.8857 (m-30) cc_final: 0.8411 (t70) REVERT: A 671 SER cc_start: 0.7618 (OUTLIER) cc_final: 0.7121 (p) REVERT: B 313 PHE cc_start: 0.7838 (m-80) cc_final: 0.7490 (m-80) REVERT: B 407 LEU cc_start: 0.9479 (tp) cc_final: 0.9068 (tp) REVERT: B 432 TRP cc_start: 0.8370 (m-10) cc_final: 0.8009 (m-90) REVERT: B 456 ASP cc_start: 0.8836 (m-30) cc_final: 0.8399 (t70) REVERT: B 671 SER cc_start: 0.8095 (t) cc_final: 0.7703 (p) outliers start: 41 outliers final: 20 residues processed: 191 average time/residue: 0.1803 time to fit residues: 54.2822 Evaluate side-chains 186 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.0050 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN B 642 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12056 Z= 0.211 Angle : 0.665 9.356 16286 Z= 0.314 Chirality : 0.045 0.182 1812 Planarity : 0.004 0.045 2060 Dihedral : 6.591 124.665 1582 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.50 % Allowed : 17.25 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.66 (0.23), residues: 1452 helix: 0.92 (0.24), residues: 502 sheet: -0.25 (0.35), residues: 204 loop : 0.49 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 432 HIS 0.006 0.001 HIS A 819 PHE 0.012 0.001 PHE A 530 TYR 0.012 0.001 TYR A 413 ARG 0.003 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.393 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 403 LEU cc_start: 0.8896 (tp) cc_final: 0.8665 (tt) REVERT: A 456 ASP cc_start: 0.8863 (m-30) cc_final: 0.8394 (t70) REVERT: A 522 CYS cc_start: 0.7629 (p) cc_final: 0.7423 (p) REVERT: A 671 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7508 (p) REVERT: A 841 PHE cc_start: 0.8822 (t80) cc_final: 0.8578 (t80) REVERT: B 313 PHE cc_start: 0.7869 (m-80) cc_final: 0.7624 (m-80) REVERT: B 403 LEU cc_start: 0.8872 (tp) cc_final: 0.8598 (tt) REVERT: B 432 TRP cc_start: 0.8514 (m-10) cc_final: 0.8125 (m-90) REVERT: B 522 CYS cc_start: 0.7618 (p) cc_final: 0.7314 (p) REVERT: B 671 SER cc_start: 0.8197 (t) cc_final: 0.7873 (p) outliers start: 46 outliers final: 28 residues processed: 191 average time/residue: 0.1838 time to fit residues: 54.9958 Evaluate side-chains 194 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12056 Z= 0.367 Angle : 0.761 9.633 16286 Z= 0.376 Chirality : 0.048 0.213 1812 Planarity : 0.005 0.047 2060 Dihedral : 6.726 108.687 1582 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.86 % Allowed : 17.55 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.17 (0.23), residues: 1452 helix: 0.57 (0.23), residues: 516 sheet: -0.81 (0.35), residues: 202 loop : 0.22 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 432 HIS 0.008 0.001 HIS B 309 PHE 0.022 0.003 PHE A 530 TYR 0.016 0.002 TYR B 593 ARG 0.004 0.001 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 162 time to evaluate : 1.396 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 403 LEU cc_start: 0.8801 (tp) cc_final: 0.8547 (tt) REVERT: A 522 CYS cc_start: 0.7735 (p) cc_final: 0.7338 (p) REVERT: A 524 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7720 (m90) REVERT: A 572 ASP cc_start: 0.8364 (t0) cc_final: 0.8125 (t0) REVERT: A 635 MET cc_start: 0.7796 (tpt) cc_final: 0.7474 (tpt) REVERT: B 403 LEU cc_start: 0.8734 (tp) cc_final: 0.8490 (tt) REVERT: B 522 CYS cc_start: 0.7697 (p) cc_final: 0.7326 (p) REVERT: B 524 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7753 (m90) REVERT: B 635 MET cc_start: 0.7769 (tpt) cc_final: 0.7455 (tpt) outliers start: 64 outliers final: 47 residues processed: 197 average time/residue: 0.1919 time to fit residues: 58.3734 Evaluate side-chains 205 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 156 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 HIS Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 HIS ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12056 Z= 0.289 Angle : 0.722 11.329 16286 Z= 0.346 Chirality : 0.046 0.221 1812 Planarity : 0.004 0.051 2060 Dihedral : 6.349 94.814 1582 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.50 % Allowed : 19.98 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.11 (0.23), residues: 1452 helix: 0.64 (0.23), residues: 512 sheet: -0.82 (0.36), residues: 198 loop : 0.09 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 432 HIS 0.005 0.001 HIS B 309 PHE 0.015 0.002 PHE A 530 TYR 0.013 0.002 TYR B 740 ARG 0.003 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8713 (pp) REVERT: A 351 LEU cc_start: 0.8108 (tt) cc_final: 0.7824 (tp) REVERT: A 403 LEU cc_start: 0.8705 (tp) cc_final: 0.8481 (mm) REVERT: A 433 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 522 CYS cc_start: 0.7702 (p) cc_final: 0.7162 (p) REVERT: A 572 ASP cc_start: 0.8330 (t0) cc_final: 0.8070 (t70) REVERT: A 879 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8441 (tt) REVERT: B 351 LEU cc_start: 0.7564 (tp) cc_final: 0.6948 (tt) REVERT: B 403 LEU cc_start: 0.8766 (tp) cc_final: 0.8541 (mm) REVERT: B 522 CYS cc_start: 0.7666 (p) cc_final: 0.7087 (p) REVERT: B 572 ASP cc_start: 0.8345 (t0) cc_final: 0.8051 (t70) outliers start: 46 outliers final: 39 residues processed: 184 average time/residue: 0.1916 time to fit residues: 54.4058 Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 141 optimal weight: 0.0670 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 HIS B 668 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12056 Z= 0.177 Angle : 0.684 14.020 16286 Z= 0.316 Chirality : 0.045 0.310 1812 Planarity : 0.004 0.059 2060 Dihedral : 5.889 81.763 1582 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.04 % Allowed : 20.67 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.25 (0.23), residues: 1452 helix: 0.78 (0.24), residues: 514 sheet: -0.73 (0.36), residues: 198 loop : 0.13 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 432 HIS 0.004 0.001 HIS A 524 PHE 0.016 0.001 PHE B 841 TYR 0.015 0.001 TYR B 740 ARG 0.008 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8688 (pp) REVERT: A 403 LEU cc_start: 0.8647 (tp) cc_final: 0.8422 (tt) REVERT: A 410 CYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9067 (p) REVERT: A 522 CYS cc_start: 0.7650 (p) cc_final: 0.7126 (p) REVERT: B 403 LEU cc_start: 0.8656 (tp) cc_final: 0.8408 (tt) REVERT: B 522 CYS cc_start: 0.7635 (p) cc_final: 0.7143 (p) outliers start: 40 outliers final: 29 residues processed: 193 average time/residue: 0.2021 time to fit residues: 59.7055 Evaluate side-chains 194 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 20.0000 chunk 15 optimal weight: 0.3980 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12056 Z= 0.218 Angle : 0.722 14.645 16286 Z= 0.335 Chirality : 0.046 0.328 1812 Planarity : 0.004 0.052 2060 Dihedral : 5.860 79.350 1580 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.03 % Allowed : 21.05 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.17 (0.23), residues: 1452 helix: 0.74 (0.23), residues: 516 sheet: -0.84 (0.35), residues: 198 loop : 0.08 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 432 HIS 0.004 0.001 HIS B 309 PHE 0.016 0.002 PHE A 841 TYR 0.013 0.001 TYR B 740 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 165 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8683 (pp) REVERT: A 403 LEU cc_start: 0.8620 (tp) cc_final: 0.8393 (tt) REVERT: A 410 CYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9009 (p) REVERT: A 522 CYS cc_start: 0.7691 (p) cc_final: 0.7096 (p) REVERT: A 711 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: B 323 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8699 (pp) REVERT: B 403 LEU cc_start: 0.8663 (tp) cc_final: 0.8402 (tt) REVERT: B 522 CYS cc_start: 0.7697 (p) cc_final: 0.7118 (p) REVERT: B 635 MET cc_start: 0.7699 (tpt) cc_final: 0.7456 (tpt) REVERT: B 711 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7607 (m-40) outliers start: 53 outliers final: 38 residues processed: 192 average time/residue: 0.1832 time to fit residues: 54.5950 Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12056 Z= 0.170 Angle : 0.723 15.737 16286 Z= 0.327 Chirality : 0.046 0.355 1812 Planarity : 0.004 0.050 2060 Dihedral : 5.637 68.082 1580 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.96 % Allowed : 22.42 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.21 (0.23), residues: 1452 helix: 0.77 (0.24), residues: 514 sheet: -0.76 (0.35), residues: 198 loop : 0.10 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 432 HIS 0.003 0.001 HIS A 524 PHE 0.018 0.001 PHE B 841 TYR 0.016 0.001 TYR B 740 ARG 0.005 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8665 (pp) REVERT: A 410 CYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9032 (p) REVERT: A 522 CYS cc_start: 0.7714 (p) cc_final: 0.7154 (p) REVERT: A 584 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: A 711 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7684 (m-40) REVERT: B 323 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8707 (pp) REVERT: B 351 LEU cc_start: 0.7526 (tt) cc_final: 0.6995 (tp) REVERT: B 403 LEU cc_start: 0.8568 (tp) cc_final: 0.8338 (tt) REVERT: B 522 CYS cc_start: 0.7672 (p) cc_final: 0.7142 (p) outliers start: 39 outliers final: 27 residues processed: 192 average time/residue: 0.1925 time to fit residues: 57.4511 Evaluate side-chains 198 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 40 optimal weight: 0.0010 chunk 118 optimal weight: 0.0570 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12056 Z= 0.256 Angle : 0.769 15.746 16286 Z= 0.355 Chirality : 0.047 0.346 1812 Planarity : 0.004 0.048 2060 Dihedral : 5.841 66.557 1580 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.34 % Allowed : 22.26 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.13 (0.23), residues: 1452 helix: 0.77 (0.23), residues: 514 sheet: -1.02 (0.35), residues: 198 loop : 0.07 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 798 HIS 0.005 0.001 HIS A 309 PHE 0.019 0.002 PHE A 841 TYR 0.011 0.002 TYR A 518 ARG 0.004 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 171 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.8177 (tt) cc_final: 0.7686 (tp) REVERT: A 410 CYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9002 (p) REVERT: A 522 CYS cc_start: 0.7631 (p) cc_final: 0.6942 (p) REVERT: A 711 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7519 (m-40) REVERT: A 844 MET cc_start: 0.7389 (tmm) cc_final: 0.7175 (tmm) REVERT: B 323 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8707 (pp) REVERT: B 351 LEU cc_start: 0.7658 (tt) cc_final: 0.7271 (tp) REVERT: B 403 LEU cc_start: 0.8563 (tp) cc_final: 0.8325 (tt) REVERT: B 522 CYS cc_start: 0.7639 (p) cc_final: 0.6944 (p) outliers start: 44 outliers final: 35 residues processed: 193 average time/residue: 0.1891 time to fit residues: 56.3412 Evaluate side-chains 201 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.0570 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12056 Z= 0.177 Angle : 0.763 16.098 16286 Z= 0.342 Chirality : 0.046 0.380 1812 Planarity : 0.004 0.049 2060 Dihedral : 5.696 56.956 1580 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.28 % Allowed : 23.56 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.23 (0.23), residues: 1452 helix: 0.76 (0.24), residues: 516 sheet: -0.80 (0.35), residues: 198 loop : 0.15 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 432 HIS 0.008 0.001 HIS A 539 PHE 0.019 0.001 PHE B 841 TYR 0.016 0.001 TYR B 740 ARG 0.004 0.000 ARG A 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8676 (pp) REVERT: A 351 LEU cc_start: 0.8115 (tt) cc_final: 0.7894 (tp) REVERT: A 410 CYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8996 (p) REVERT: A 522 CYS cc_start: 0.7666 (p) cc_final: 0.7074 (p) REVERT: A 711 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7654 (m-40) REVERT: A 844 MET cc_start: 0.7405 (tmm) cc_final: 0.7191 (tmm) REVERT: B 323 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8716 (pp) REVERT: B 351 LEU cc_start: 0.7604 (tt) cc_final: 0.7207 (tp) REVERT: B 522 CYS cc_start: 0.7613 (p) cc_final: 0.7052 (p) outliers start: 30 outliers final: 25 residues processed: 187 average time/residue: 0.1939 time to fit residues: 56.0730 Evaluate side-chains 195 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 874 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 106 optimal weight: 8.9990 chunk 17 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 119 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.106460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078401 restraints weight = 34299.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.081567 restraints weight = 18056.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083698 restraints weight = 12084.413| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12056 Z= 0.164 Angle : 0.766 16.348 16286 Z= 0.339 Chirality : 0.046 0.375 1812 Planarity : 0.004 0.047 2060 Dihedral : 5.477 54.994 1580 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.05 % Allowed : 23.86 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.24 (0.23), residues: 1452 helix: 0.76 (0.24), residues: 516 sheet: -0.71 (0.35), residues: 198 loop : 0.13 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 432 HIS 0.009 0.001 HIS A 539 PHE 0.020 0.001 PHE A 841 TYR 0.009 0.001 TYR B 740 ARG 0.004 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.18 seconds wall clock time: 42 minutes 20.11 seconds (2540.11 seconds total)