Starting phenix.real_space_refine on Mon Mar 18 03:39:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ca3_30323/03_2024/7ca3_30323_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 8 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: 6 Type Number sf(0) Gaussians S 58 5.16 5 C 6861 2.51 5 N 1744 2.21 5 O 1889 1.98 5 F 3 1.80 5 H 9307 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 384": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B GLU 626": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19862 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 9628 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 27, 'TRANS': 641} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 10127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10127 Classifications: {'peptide': 681} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 651} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'FN0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.00, per 1000 atoms: 0.45 Number of scatterers: 19862 At special positions: 0 Unit cell: (156.87, 149.4, 101.26, 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) S 58 16.00 F 3 9.00 O 1889 8.00 N 1744 7.00 C 6861 6.00 H 9307 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.04 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=1.52 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=3.00 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.97 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 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: 15.22 Conformation dependent library (CDL) restraints added in 2.1 seconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2526 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 8 sheets defined 48.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 186 through 200 Proline residue: A 190 - end of helix removed outlier: 3.790A pdb=" N VAL A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.856A pdb=" N GLU A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N MET A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 Processing helix chain 'A' and resid 290 through 303 Proline residue: A 295 - end of helix removed outlier: 4.058A pdb=" N VAL A 298 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.972A pdb=" N SER A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.645A pdb=" N ARG A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 4.741A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 467 through 484 removed outlier: 5.453A pdb=" N ILE A 474 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 Processing helix chain 'A' and resid 589 through 615 removed outlier: 3.896A pdb=" N ILE A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 628 through 647 removed outlier: 4.455A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 660 through 690 removed outlier: 4.395A pdb=" N ALA A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU A 667 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 729 removed outlier: 4.045A pdb=" N TRP A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 790 removed outlier: 3.711A pdb=" N PHE A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 827 removed outlier: 3.649A pdb=" N MET A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 815 " --> pdb=" O ASN A 811 " (cutoff:3.500A) Proline residue: A 821 - end of helix removed outlier: 3.659A pdb=" N SER A 827 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 837 removed outlier: 4.580A pdb=" N PHE A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA A 835 " --> pdb=" O ASP A 831 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 removed outlier: 3.810A pdb=" N ILE A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 860 removed outlier: 4.380A pdb=" N PHE A 853 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 854 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Proline residue: A 855 - end of helix Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 136 through 145 removed outlier: 4.838A pdb=" N GLU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.538A pdb=" N VAL B 182 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 183 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 184 - end of helix Processing helix chain 'B' and resid 206 through 218 removed outlier: 4.596A pdb=" N VAL B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 removed outlier: 4.116A pdb=" N ASN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 removed outlier: 4.145A pdb=" N ALA B 261 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 264 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR B 268 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 335 through 345 Processing helix chain 'B' and resid 356 through 373 Processing helix chain 'B' and resid 378 through 384 removed outlier: 4.363A pdb=" N GLN B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 484 through 504 Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 518 through 537 removed outlier: 4.387A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 582 removed outlier: 3.606A pdb=" N VAL B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU B 560 " --> pdb=" O ARG B 556 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 615 removed outlier: 3.879A pdb=" N LEU B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 680 removed outlier: 4.036A pdb=" N LEU B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 675 " --> pdb=" O GLY B 671 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 680 " --> pdb=" O TRP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 689 through 713 removed outlier: 3.719A pdb=" N MET B 694 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 745 removed outlier: 3.862A pdb=" N VAL B 724 " --> pdb=" O GLN B 720 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 725 " --> pdb=" O PHE B 721 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 728 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Proline residue: B 742 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 264 through 266 Processing sheet with id= B, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.443A pdb=" N VAL A 389 " --> pdb=" O ILE A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 423 through 427 Processing sheet with id= D, first strand: chain 'A' and resid 551 through 554 Processing sheet with id= E, first strand: chain 'A' and resid 738 through 740 Processing sheet with id= F, first strand: chain 'B' and resid 98 through 105 removed outlier: 3.639A pdb=" N MET B 62 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET B 129 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 152 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLY B 132 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU B 154 " --> pdb=" O GLY B 132 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 250 through 252 removed outlier: 6.555A pdb=" N GLN B 278 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 315 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 408 through 410 removed outlier: 3.759A pdb=" N PHE B 408 " --> pdb=" O VAL B 415 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1092 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: 6.77 Time building geometry restraints manager: 15.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9294 1.02 - 1.23: 40 1.23 - 1.43: 4586 1.43 - 1.63: 6101 1.63 - 1.83: 92 Bond restraints: 20113 Sorted by residual: bond pdb=" C THR B 654 " pdb=" N ILE B 655 " ideal model delta sigma weight residual 1.331 1.478 -0.147 1.01e-02 9.80e+03 2.13e+02 bond pdb=" N LEU A 852 " pdb=" H LEU A 852 " ideal model delta sigma weight residual 0.860 1.072 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C SER B 137 " pdb=" N VAL B 138 " ideal model delta sigma weight residual 1.334 1.462 -0.128 1.26e-02 6.30e+03 1.03e+02 bond pdb=" C6 FN0 B 902 " pdb=" O1 FN0 B 902 " ideal model delta sigma weight residual 1.514 1.383 0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" ND2 ASN B 443 " pdb="HD22 ASN B 443 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 20108 not shown) Histogram of bond angle deviations from ideal: 60.14 - 75.58: 22 75.58 - 91.03: 26 91.03 - 106.47: 777 106.47 - 121.91: 31349 121.91 - 137.35: 3622 Bond angle restraints: 35796 Sorted by residual: angle pdb=" C VAL B 719 " pdb=" N GLN B 720 " pdb=" H GLN B 720 " ideal model delta sigma weight residual 124.96 69.19 55.77 3.00e+00 1.11e-01 3.46e+02 angle pdb=" CA GLN B 720 " pdb=" N GLN B 720 " pdb=" H GLN B 720 " ideal model delta sigma weight residual 114.66 60.14 54.52 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA GLN B 386 " pdb=" N GLN B 386 " pdb=" H GLN B 386 " ideal model delta sigma weight residual 114.63 62.89 51.74 3.00e+00 1.11e-01 2.97e+02 angle pdb=" C ILE B 385 " pdb=" N GLN B 386 " pdb=" H GLN B 386 " ideal model delta sigma weight residual 124.93 74.46 50.47 3.00e+00 1.11e-01 2.83e+02 angle pdb=" N ASP B 608 " pdb=" CA ASP B 608 " pdb=" HA ASP B 608 " ideal model delta sigma weight residual 110.00 68.17 41.83 3.00e+00 1.11e-01 1.94e+02 ... (remaining 35791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8225 17.82 - 35.64: 1160 35.64 - 53.45: 309 53.45 - 71.27: 73 71.27 - 89.09: 16 Dihedral angle restraints: 9783 sinusoidal: 5140 harmonic: 4643 Sorted by residual: dihedral pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " pdb=" SG CYS B 266 " pdb=" CB CYS B 266 " ideal model delta sinusoidal sigma weight residual -86.00 -4.77 -81.23 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" C TYR A 234 " pdb=" N TYR A 234 " pdb=" CA TYR A 234 " pdb=" CB TYR A 234 " ideal model delta harmonic sigma weight residual -122.60 -143.85 21.25 0 2.50e+00 1.60e-01 7.22e+01 dihedral pdb=" C VAL A 851 " pdb=" N VAL A 851 " pdb=" CA VAL A 851 " pdb=" CB VAL A 851 " ideal model delta harmonic sigma weight residual -122.00 -140.89 18.89 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 9780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.098: 1678 1.098 - 2.197: 3 2.197 - 3.295: 0 3.295 - 4.394: 0 4.394 - 5.492: 1 Chirality restraints: 1682 Sorted by residual: chirality pdb=" C7 FN0 B 902 " pdb=" C13 FN0 B 902 " pdb=" C17 FN0 B 902 " pdb=" C5 FN0 B 902 " both_signs ideal model delta sigma weight residual False -2.69 2.80 -5.49 2.00e-01 2.50e+01 7.54e+02 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 0.78 1.86 2.00e-01 2.50e+01 8.69e+01 chirality pdb=" CG LEU B 609 " pdb=" CB LEU B 609 " pdb=" CD1 LEU B 609 " pdb=" CD2 LEU B 609 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.31e+01 ... (remaining 1679 not shown) Planarity restraints: 2949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 851 " -0.123 2.00e-02 2.50e+03 2.07e-01 4.28e+02 pdb=" N LEU A 852 " 0.358 2.00e-02 2.50e+03 pdb=" CA LEU A 852 " -0.114 2.00e-02 2.50e+03 pdb=" H LEU A 852 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 654 " 0.054 2.00e-02 2.50e+03 1.28e-01 1.64e+02 pdb=" N ILE B 655 " -0.218 2.00e-02 2.50e+03 pdb=" CA ILE B 655 " 0.052 2.00e-02 2.50e+03 pdb=" H ILE B 655 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 852 " -0.043 2.00e-02 2.50e+03 8.10e-02 6.56e+01 pdb=" N PHE A 853 " 0.139 2.00e-02 2.50e+03 pdb=" CA PHE A 853 " -0.036 2.00e-02 2.50e+03 pdb=" H PHE A 853 " -0.061 2.00e-02 2.50e+03 ... (remaining 2946 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 103 1.79 - 2.49: 15918 2.49 - 3.20: 58637 3.20 - 3.90: 70142 3.90 - 4.60: 108994 Nonbonded interactions: 253794 Sorted by model distance: nonbonded pdb=" H THR B 238 " pdb=" H SER B 239 " model vdw 1.089 2.100 nonbonded pdb=" O PRO A 237 " pdb=" HZ1 LYS A 239 " model vdw 1.281 1.850 nonbonded pdb=" O PRO A 237 " pdb=" HZ3 LYS A 239 " model vdw 1.347 1.850 nonbonded pdb=" O PRO A 237 " pdb=" NZ LYS A 239 " model vdw 1.348 2.350 nonbonded pdb=" HD2 TYR A 171 " pdb=" HG2 PRO A 237 " model vdw 1.399 2.270 ... (remaining 253789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.300 Extract box with map and model: 6.420 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 61.320 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.017 0.153 10806 Z= 1.106 Angle : 1.297 16.915 14704 Z= 0.750 Chirality : 0.173 5.492 1682 Planarity : 0.008 0.067 1824 Dihedral : 15.542 89.087 3989 Min Nonbonded Distance : 1.348 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 15.19 % Favored : 84.21 % Rotamer: Outliers : 1.01 % Allowed : 10.84 % Favored : 88.15 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 1.79 % 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: -4.98 (0.19), residues: 1336 helix: -2.84 (0.15), residues: 612 sheet: -3.63 (0.32), residues: 159 loop : -3.64 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 558 HIS 0.012 0.003 HIS A 735 PHE 0.045 0.004 PHE A 366 TYR 0.044 0.004 TYR B 314 ARG 0.010 0.001 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 1.543 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: 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 417 GLU cc_start: 0.8639 (pt0) cc_final: 0.8343 (tm-30) REVERT: A 441 MET cc_start: 0.8393 (mmm) cc_final: 0.7571 (mmm) REVERT: A 446 PHE cc_start: 0.9441 (t80) cc_final: 0.9219 (t80) REVERT: A 465 GLN cc_start: 0.8886 (mm110) cc_final: 0.8675 (tp-100) REVERT: A 834 PHE cc_start: 0.7166 (t80) cc_final: 0.6918 (t80) REVERT: B 82 GLU cc_start: 0.9491 (mp0) cc_final: 0.9215 (mp0) REVERT: B 144 GLU cc_start: 0.8547 (pt0) cc_final: 0.8292 (pt0) REVERT: B 485 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5868 (pp) REVERT: B 524 ILE cc_start: 0.6587 (pt) cc_final: 0.6187 (pt) outliers start: 11 outliers final: 6 residues processed: 204 average time/residue: 0.4293 time to fit residues: 125.3149 Evaluate side-chains 154 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 40.0000 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 314 GLN A 444 GLN A 618 HIS A 664 GLN B 87 GLN B 110 ASN B 150 ASN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 337 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 HIS ** B 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10806 Z= 0.221 Angle : 0.859 26.446 14704 Z= 0.427 Chirality : 0.101 2.190 1682 Planarity : 0.005 0.057 1824 Dihedral : 8.008 88.641 1652 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.23 % Favored : 88.70 % Rotamer: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.24 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.20), residues: 1336 helix: -2.06 (0.18), residues: 641 sheet: -2.84 (0.35), residues: 166 loop : -3.51 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 558 HIS 0.003 0.001 HIS B 393 PHE 0.019 0.002 PHE B 319 TYR 0.013 0.001 TYR A 846 ARG 0.006 0.001 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 417 GLU cc_start: 0.8497 (pt0) cc_final: 0.8242 (tm-30) REVERT: A 610 LEU cc_start: 0.5583 (tp) cc_final: 0.5157 (tp) REVERT: A 834 PHE cc_start: 0.6887 (t80) cc_final: 0.6500 (t80) REVERT: A 839 LEU cc_start: 0.7009 (mp) cc_final: 0.6770 (mt) REVERT: B 104 TYR cc_start: 0.8903 (m-80) cc_final: 0.8572 (m-80) REVERT: B 213 ASN cc_start: 0.9027 (m-40) cc_final: 0.8643 (t0) REVERT: B 235 ASP cc_start: 0.9039 (t0) cc_final: 0.8747 (t0) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.4148 time to fit residues: 117.9928 Evaluate side-chains 148 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 30.0000 chunk 131 optimal weight: 0.7980 chunk 108 optimal weight: 0.0070 chunk 120 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 501 ASN B 87 GLN B 246 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10806 Z= 0.201 Angle : 0.782 26.748 14704 Z= 0.381 Chirality : 0.097 1.937 1682 Planarity : 0.004 0.048 1824 Dihedral : 7.365 89.037 1652 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.98 % Favored : 87.95 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.22), residues: 1336 helix: -1.48 (0.19), residues: 634 sheet: -2.72 (0.36), residues: 182 loop : -3.22 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 PHE 0.015 0.001 PHE B 319 TYR 0.015 0.001 TYR A 379 ARG 0.002 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.576 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: symmetry clash REVERT: A 194 MET cc_start: 0.8749 (ttt) cc_final: 0.8460 (tmm) REVERT: A 417 GLU cc_start: 0.8510 (pt0) cc_final: 0.8233 (tm-30) REVERT: B 213 ASN cc_start: 0.8899 (m-40) cc_final: 0.8385 (t0) REVERT: B 235 ASP cc_start: 0.9116 (t0) cc_final: 0.8817 (t0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3864 time to fit residues: 110.8902 Evaluate side-chains 147 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10806 Z= 0.275 Angle : 0.817 27.631 14704 Z= 0.403 Chirality : 0.097 1.865 1682 Planarity : 0.005 0.055 1824 Dihedral : 7.326 86.511 1652 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.02 % Favored : 86.83 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.22), residues: 1336 helix: -1.23 (0.20), residues: 623 sheet: -2.54 (0.35), residues: 188 loop : -3.11 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 395 HIS 0.006 0.001 HIS A 802 PHE 0.014 0.001 PHE A 853 TYR 0.013 0.001 TYR A 379 ARG 0.005 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 ASN cc_start: 0.9149 (p0) cc_final: 0.8949 (p0) REVERT: A 417 GLU cc_start: 0.8470 (pt0) cc_final: 0.8252 (tm-30) REVERT: A 834 PHE cc_start: 0.7258 (t80) cc_final: 0.7025 (t80) REVERT: B 213 ASN cc_start: 0.9050 (m-40) cc_final: 0.8651 (t0) REVERT: B 235 ASP cc_start: 0.9123 (t0) cc_final: 0.8853 (t0) REVERT: B 553 CYS cc_start: 0.7368 (m) cc_final: 0.7152 (m) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3961 time to fit residues: 104.5795 Evaluate side-chains 143 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 246 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10806 Z= 0.248 Angle : 0.773 26.154 14704 Z= 0.379 Chirality : 0.098 2.030 1682 Planarity : 0.005 0.068 1824 Dihedral : 7.165 89.293 1652 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.72 % Favored : 87.20 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.22), residues: 1336 helix: -1.14 (0.20), residues: 626 sheet: -2.23 (0.37), residues: 185 loop : -3.10 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 395 HIS 0.004 0.001 HIS A 735 PHE 0.014 0.001 PHE B 499 TYR 0.014 0.001 TYR A 379 ARG 0.008 0.000 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.685 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: A 198 ASP cc_start: 0.9160 (t70) cc_final: 0.8955 (t0) REVERT: A 399 ASN cc_start: 0.9160 (p0) cc_final: 0.8942 (p0) REVERT: A 417 GLU cc_start: 0.8521 (pt0) cc_final: 0.8285 (tm-30) REVERT: A 834 PHE cc_start: 0.7304 (t80) cc_final: 0.6992 (t80) REVERT: B 213 ASN cc_start: 0.9027 (m-40) cc_final: 0.8697 (m-40) REVERT: B 235 ASP cc_start: 0.9114 (t0) cc_final: 0.8861 (t0) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.4032 time to fit residues: 105.8597 Evaluate side-chains 142 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 68 optimal weight: 0.4980 chunk 124 optimal weight: 8.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN A 811 ASN B 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10806 Z= 0.275 Angle : 0.789 26.553 14704 Z= 0.387 Chirality : 0.097 1.971 1682 Planarity : 0.005 0.051 1824 Dihedral : 7.091 89.231 1652 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.32 % Favored : 86.60 % Rotamer: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.26 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.22), residues: 1336 helix: -1.11 (0.20), residues: 632 sheet: -2.29 (0.37), residues: 193 loop : -3.15 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 395 HIS 0.006 0.001 HIS A 735 PHE 0.011 0.001 PHE B 319 TYR 0.036 0.002 TYR B 697 ARG 0.007 0.000 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 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: 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 178 MET cc_start: 0.8525 (mmt) cc_final: 0.8069 (mmm) REVERT: A 243 MET cc_start: 0.8381 (mmm) cc_final: 0.8071 (mmm) REVERT: A 265 LEU cc_start: 0.9535 (tp) cc_final: 0.9130 (tp) REVERT: A 834 PHE cc_start: 0.7345 (t80) cc_final: 0.6982 (t80) REVERT: B 62 MET cc_start: 0.8718 (ptp) cc_final: 0.8259 (pmm) REVERT: B 82 GLU cc_start: 0.9496 (mp0) cc_final: 0.9217 (mp0) REVERT: B 213 ASN cc_start: 0.9030 (m-40) cc_final: 0.8737 (m-40) REVERT: B 235 ASP cc_start: 0.9108 (t0) cc_final: 0.8855 (t0) REVERT: B 553 CYS cc_start: 0.7360 (m) cc_final: 0.6949 (m) outliers start: 1 outliers final: 1 residues processed: 175 average time/residue: 0.3873 time to fit residues: 100.9160 Evaluate side-chains 143 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.7071 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10806 Z= 0.204 Angle : 0.750 26.275 14704 Z= 0.363 Chirality : 0.097 1.983 1682 Planarity : 0.004 0.045 1824 Dihedral : 6.896 89.190 1652 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.68 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1336 helix: -0.93 (0.20), residues: 636 sheet: -2.15 (0.38), residues: 193 loop : -3.01 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 395 HIS 0.003 0.001 HIS A 735 PHE 0.011 0.001 PHE A 446 TYR 0.015 0.001 TYR A 379 ARG 0.005 0.000 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.677 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: A 178 MET cc_start: 0.8528 (mmt) cc_final: 0.8062 (mmm) REVERT: A 243 MET cc_start: 0.8329 (mmm) cc_final: 0.8063 (mmm) REVERT: A 265 LEU cc_start: 0.9539 (tp) cc_final: 0.9137 (tp) REVERT: A 595 VAL cc_start: 0.8947 (m) cc_final: 0.8728 (m) REVERT: A 785 ILE cc_start: 0.8435 (pt) cc_final: 0.8231 (pt) REVERT: A 809 ILE cc_start: 0.8162 (tp) cc_final: 0.7951 (tt) REVERT: A 834 PHE cc_start: 0.7296 (t80) cc_final: 0.6889 (t80) REVERT: B 62 MET cc_start: 0.8707 (ptp) cc_final: 0.8251 (pmm) REVERT: B 213 ASN cc_start: 0.8943 (m-40) cc_final: 0.8713 (m-40) REVERT: B 235 ASP cc_start: 0.9113 (t0) cc_final: 0.8839 (t0) REVERT: B 553 CYS cc_start: 0.7237 (m) cc_final: 0.6848 (m) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3986 time to fit residues: 106.3538 Evaluate side-chains 143 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 123 optimal weight: 0.0010 chunk 112 optimal weight: 9.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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: 0.7047 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10806 Z= 0.164 Angle : 0.732 26.214 14704 Z= 0.351 Chirality : 0.098 2.056 1682 Planarity : 0.004 0.044 1824 Dihedral : 6.644 89.633 1652 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.78 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.23), residues: 1336 helix: -0.73 (0.20), residues: 632 sheet: -1.92 (0.39), residues: 189 loop : -2.82 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS A 802 PHE 0.010 0.001 PHE B 730 TYR 0.014 0.001 TYR A 379 ARG 0.004 0.000 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8515 (mmt) cc_final: 0.8013 (mmm) REVERT: A 221 ASP cc_start: 0.9418 (t0) cc_final: 0.9146 (t0) REVERT: A 243 MET cc_start: 0.8316 (mmm) cc_final: 0.8077 (mmm) REVERT: A 265 LEU cc_start: 0.9525 (tp) cc_final: 0.9115 (tp) REVERT: A 785 ILE cc_start: 0.8380 (pt) cc_final: 0.8179 (pt) REVERT: A 834 PHE cc_start: 0.7250 (t80) cc_final: 0.6986 (t80) REVERT: B 62 MET cc_start: 0.8735 (ptp) cc_final: 0.8266 (pmm) REVERT: B 82 GLU cc_start: 0.9486 (mp0) cc_final: 0.9178 (mp0) REVERT: B 213 ASN cc_start: 0.8848 (m-40) cc_final: 0.8601 (m-40) REVERT: B 235 ASP cc_start: 0.9114 (t0) cc_final: 0.8830 (t0) REVERT: B 553 CYS cc_start: 0.7153 (m) cc_final: 0.6778 (m) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.4021 time to fit residues: 105.7551 Evaluate side-chains 145 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 0.0050 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10806 Z= 0.158 Angle : 0.729 26.450 14704 Z= 0.347 Chirality : 0.097 1.968 1682 Planarity : 0.004 0.043 1824 Dihedral : 6.467 89.458 1652 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.48 % Favored : 89.45 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.23), residues: 1336 helix: -0.47 (0.21), residues: 628 sheet: -1.85 (0.39), residues: 189 loop : -2.80 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.001 HIS B 393 PHE 0.010 0.001 PHE A 375 TYR 0.014 0.001 TYR B 531 ARG 0.005 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8513 (mmt) cc_final: 0.8018 (mmm) REVERT: A 221 ASP cc_start: 0.9320 (t0) cc_final: 0.9090 (t0) REVERT: A 243 MET cc_start: 0.8300 (mmm) cc_final: 0.8063 (mmm) REVERT: A 265 LEU cc_start: 0.9510 (tp) cc_final: 0.9119 (tp) REVERT: A 399 ASN cc_start: 0.9100 (p0) cc_final: 0.8884 (p0) REVERT: A 595 VAL cc_start: 0.8968 (m) cc_final: 0.8756 (m) REVERT: A 785 ILE cc_start: 0.8326 (pt) cc_final: 0.8056 (pt) REVERT: A 834 PHE cc_start: 0.7183 (t80) cc_final: 0.6874 (t80) REVERT: B 62 MET cc_start: 0.8723 (ptp) cc_final: 0.8269 (pmm) REVERT: B 82 GLU cc_start: 0.9465 (mp0) cc_final: 0.9185 (mp0) REVERT: B 144 GLU cc_start: 0.8365 (pt0) cc_final: 0.8057 (pt0) REVERT: B 213 ASN cc_start: 0.8801 (m-40) cc_final: 0.8600 (m-40) REVERT: B 235 ASP cc_start: 0.9127 (t0) cc_final: 0.8846 (t0) REVERT: B 553 CYS cc_start: 0.7168 (m) cc_final: 0.6757 (m) REVERT: B 737 CYS cc_start: 0.3982 (t) cc_final: 0.3652 (t) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3793 time to fit residues: 99.5111 Evaluate side-chains 140 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.0370 chunk 60 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10806 Z= 0.144 Angle : 0.724 26.604 14704 Z= 0.343 Chirality : 0.096 1.948 1682 Planarity : 0.004 0.041 1824 Dihedral : 6.257 88.639 1652 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.28 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.23), residues: 1336 helix: -0.23 (0.21), residues: 630 sheet: -1.73 (0.38), residues: 189 loop : -2.71 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.000 HIS B 393 PHE 0.009 0.001 PHE B 730 TYR 0.012 0.001 TYR B 691 ARG 0.003 0.000 ARG B 556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8473 (mmt) cc_final: 0.7973 (mmm) REVERT: A 265 LEU cc_start: 0.9499 (tp) cc_final: 0.9118 (tp) REVERT: A 471 TYR cc_start: 0.8069 (t80) cc_final: 0.7699 (t80) REVERT: A 595 VAL cc_start: 0.8922 (m) cc_final: 0.8714 (m) REVERT: A 785 ILE cc_start: 0.8264 (pt) cc_final: 0.7930 (pt) REVERT: A 834 PHE cc_start: 0.7110 (t80) cc_final: 0.6826 (t80) REVERT: B 62 MET cc_start: 0.8680 (ptp) cc_final: 0.8273 (pmm) REVERT: B 82 GLU cc_start: 0.9485 (mp0) cc_final: 0.9176 (mp0) REVERT: B 99 LEU cc_start: 0.8420 (tt) cc_final: 0.8045 (tt) REVERT: B 100 ASP cc_start: 0.8238 (t0) cc_final: 0.7775 (m-30) REVERT: B 109 ASP cc_start: 0.8303 (t0) cc_final: 0.7704 (m-30) REVERT: B 235 ASP cc_start: 0.9085 (t0) cc_final: 0.8810 (t0) REVERT: B 272 MET cc_start: 0.8739 (mmt) cc_final: 0.8531 (mmt) REVERT: B 553 CYS cc_start: 0.7034 (m) cc_final: 0.6650 (m) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3999 time to fit residues: 107.3431 Evaluate side-chains 146 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 109 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 chunk 19 optimal weight: 0.5980 chunk 93 optimal weight: 0.0570 chunk 6 optimal weight: 0.4980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 GLN B 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.104435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.085027 restraints weight = 95387.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087725 restraints weight = 51047.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089564 restraints weight = 32760.806| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10806 Z= 0.144 Angle : 0.716 26.887 14704 Z= 0.338 Chirality : 0.095 1.886 1682 Planarity : 0.004 0.047 1824 Dihedral : 6.093 87.580 1652 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.68 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % 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: -1.96 (0.23), residues: 1336 helix: -0.09 (0.21), residues: 630 sheet: -1.64 (0.38), residues: 189 loop : -2.69 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS B 393 PHE 0.010 0.001 PHE B 730 TYR 0.013 0.001 TYR B 531 ARG 0.003 0.000 ARG B 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.54 seconds wall clock time: 72 minutes 30.37 seconds (4350.37 seconds total)