Starting phenix.real_space_refine on Mon Mar 11 18:19:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv1_30209/03_2024/7bv1_30209.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv1_30209/03_2024/7bv1_30209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv1_30209/03_2024/7bv1_30209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv1_30209/03_2024/7bv1_30209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv1_30209/03_2024/7bv1_30209.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv1_30209/03_2024/7bv1_30209.pdb" } resolution = 2.8 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 64 5.16 5 C 5626 2.51 5 N 1460 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "C GLU 23": "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: 8799 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6724 Classifications: {'peptide': 836} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 807} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 865 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 727 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1825 SG CYS A 301 40.360 63.172 37.957 1.00 10.69 S ATOM 1866 SG CYS A 306 40.337 62.023 34.421 1.00 7.82 S ATOM 1898 SG CYS A 310 43.496 61.958 36.510 1.00 18.90 S ATOM 3300 SG CYS A 487 23.293 58.642 47.127 1.00 13.60 S ATOM 4553 SG CYS A 645 21.979 58.294 43.851 1.00 17.07 S ATOM 4559 SG CYS A 646 25.396 60.467 44.225 1.00 15.31 S Time building chain proxies: 5.07, per 1000 atoms: 0.58 Number of scatterers: 8799 At special positions: 0 Unit cell: (90.246, 93.288, 127.764, 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) Zn 2 29.99 S 64 16.00 O 1647 8.00 N 1460 7.00 C 5626 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: 3.42 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 50.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.964A pdb=" N TYR A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.620A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.630A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.351A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 248' Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.671A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.611A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.820A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.702A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.651A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.528A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.796A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.954A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.343A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.635A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.765A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.820A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 852 through 867 removed outlier: 3.683A pdb=" N ILE A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.588A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 79 through 97 removed outlier: 3.626A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.920A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.740A pdb=" N CYS B 114 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.662A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.579A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.816A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.805A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.922A pdb=" N THR D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 4.344A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.637A pdb=" N GLY A 203 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 354 removed outlier: 3.595A pdb=" N VAL A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 354 removed outlier: 3.595A pdb=" N VAL A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 7.007A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 7.007A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.768A pdb=" N ASN A 414 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AB2, first strand: chain 'D' and resid 146 through 149 removed outlier: 3.986A pdb=" N GLU D 155 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1191 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: 3.35 Time building geometry restraints manager: 3.73 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: 2798 1.34 - 1.46: 2134 1.46 - 1.59: 3963 1.59 - 1.71: 0 1.71 - 1.84: 97 Bond restraints: 8992 Sorted by residual: bond pdb=" N VAL A 662 " pdb=" CA VAL A 662 " ideal model delta sigma weight residual 1.457 1.499 -0.043 1.07e-02 8.73e+03 1.60e+01 bond pdb=" N LYS A 263 " pdb=" CA LYS A 263 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.27e+01 bond pdb=" N ILE D 166 " pdb=" CA ILE D 166 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 9.14e+00 bond pdb=" N ILE A 847 " pdb=" CA ILE A 847 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N VAL A 844 " pdb=" CA VAL A 844 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.18e-02 7.18e+03 8.85e+00 ... (remaining 8987 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.86: 167 105.86 - 112.90: 4725 112.90 - 119.94: 3226 119.94 - 126.98: 4016 126.98 - 134.02: 88 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C PRO D 121 " pdb=" CA PRO D 121 " pdb=" CB PRO D 121 " ideal model delta sigma weight residual 111.40 107.43 3.97 9.10e-01 1.21e+00 1.90e+01 angle pdb=" CA ALA A 660 " pdb=" C ALA A 660 " pdb=" O ALA A 660 " ideal model delta sigma weight residual 120.82 116.78 4.04 1.05e+00 9.07e-01 1.48e+01 angle pdb=" CA ALA D 125 " pdb=" C ALA D 125 " pdb=" O ALA D 125 " ideal model delta sigma weight residual 122.27 118.08 4.19 1.16e+00 7.43e-01 1.31e+01 angle pdb=" N GLN A 661 " pdb=" CA GLN A 661 " pdb=" C GLN A 661 " ideal model delta sigma weight residual 111.36 115.27 -3.91 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N LEU A 401 " pdb=" CA LEU A 401 " pdb=" C LEU A 401 " ideal model delta sigma weight residual 112.54 116.87 -4.33 1.22e+00 6.72e-01 1.26e+01 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 4739 18.13 - 36.25: 496 36.25 - 54.38: 87 54.38 - 72.51: 14 72.51 - 90.63: 7 Dihedral angle restraints: 5343 sinusoidal: 2045 harmonic: 3298 Sorted by residual: dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual -180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" N LEU A 758 " pdb=" CA LEU A 758 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" C ASP A 208 " pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" CB ASP A 208 " ideal model delta harmonic sigma weight residual -122.60 -131.33 8.73 0 2.50e+00 1.60e-01 1.22e+01 ... (remaining 5340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1156 0.070 - 0.140: 193 0.140 - 0.210: 32 0.210 - 0.280: 8 0.280 - 0.350: 4 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ASN A 150 " pdb=" N ASN A 150 " pdb=" C ASN A 150 " pdb=" CB ASN A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ILE D 120 " pdb=" N ILE D 120 " pdb=" C ILE D 120 " pdb=" CB ILE D 120 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE A 888 " pdb=" CA ILE A 888 " pdb=" CG1 ILE A 888 " pdb=" CG2 ILE A 888 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 1390 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 232 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 667 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C VAL A 667 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 667 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 668 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 161 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C ASP A 161 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP A 161 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP A 162 " 0.012 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2132 2.79 - 3.32: 8266 3.32 - 3.85: 13878 3.85 - 4.37: 17030 4.37 - 4.90: 28844 Nonbonded interactions: 70150 Sorted by model distance: nonbonded pdb=" OD1 ASP A 194 " pdb=" OH TYR A 289 " model vdw 2.266 2.440 nonbonded pdb=" O ASP A 684 " pdb=" OG1 THR A 687 " model vdw 2.269 2.440 nonbonded pdb=" N GLU A 136 " pdb=" OE1 GLU A 136 " model vdw 2.380 2.520 nonbonded pdb=" O PRO A 322 " pdb=" OG SER A 325 " model vdw 2.387 2.440 nonbonded pdb=" OG1 THR A 409 " pdb=" OE2 GLU C 23 " model vdw 2.392 2.440 ... (remaining 70145 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 'B' and (resid 85 through 95 or (resid 96 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 121 or (resid 122 and ( \ name N or name CA or name C or name O or name CB )) or resid 123 through 126 or \ (resid 127 and (name N or name CA or name C or name O or name CB )) or resid 128 \ through 133 or (resid 134 and (name N or name CA or name C or name O or name CB \ )) or resid 135 or (resid 136 and (name N or name CA or name C or name O or nam \ e CB )) or resid 137 through 138 or (resid 139 and (name N or name CA or name C \ or name O or name CB )) or resid 140 through 169 or resid 176 through 181 or (re \ sid 182 and (name N or name CA or name C or name O or name CB )) or resid 183 th \ rough 189)) selection = (chain 'D' and (resid 85 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 189)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.130 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.450 Find NCS groups from input model: 0.320 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.005 0.052 8992 Z= 0.327 Angle : 0.816 8.000 12222 Z= 0.527 Chirality : 0.058 0.350 1393 Planarity : 0.005 0.056 1555 Dihedral : 15.134 90.631 3209 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.91 (0.24), residues: 1095 helix: -0.92 (0.23), residues: 491 sheet: -1.23 (0.43), residues: 125 loop : -1.51 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 162 HIS 0.004 0.001 HIS A 892 PHE 0.023 0.002 PHE A 471 TYR 0.021 0.002 TYR D 138 ARG 0.004 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6846 (m-80) cc_final: 0.6589 (m-80) REVERT: A 760 ASP cc_start: 0.5906 (p0) cc_final: 0.5679 (p0) outliers start: 0 outliers final: 1 residues processed: 248 average time/residue: 1.0128 time to fit residues: 270.1120 Evaluate side-chains 162 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0970 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 98 optimal weight: 9.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 224 GLN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 773 GLN A 781 ASN A 790 ASN A 815 GLN A 872 HIS A 886 GLN A 928 HIS B 176 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8992 Z= 0.144 Angle : 0.539 6.551 12222 Z= 0.289 Chirality : 0.042 0.175 1393 Planarity : 0.004 0.073 1555 Dihedral : 4.198 19.599 1206 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.11 % Allowed : 15.98 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.03 (0.25), residues: 1095 helix: -0.15 (0.23), residues: 511 sheet: -0.66 (0.45), residues: 112 loop : -1.17 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.003 0.001 HIS A 816 PHE 0.017 0.001 PHE A 652 TYR 0.013 0.001 TYR A 289 ARG 0.003 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 271 LEU cc_start: 0.8833 (mp) cc_final: 0.8629 (mt) REVERT: A 334 PHE cc_start: 0.7044 (m-80) cc_final: 0.6654 (m-80) REVERT: A 415 PHE cc_start: 0.6773 (t80) cc_final: 0.6445 (t80) REVERT: A 508 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7688 (mmtp) REVERT: A 811 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: A 826 TYR cc_start: 0.7046 (m-80) cc_final: 0.6837 (m-80) REVERT: B 155 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: C 56 LEU cc_start: 0.7542 (tp) cc_final: 0.7335 (tp) REVERT: D 93 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7167 (p) outliers start: 30 outliers final: 9 residues processed: 184 average time/residue: 0.9201 time to fit residues: 184.0676 Evaluate side-chains 163 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 404 ASN A 543 ASN A 599 HIS A 698 GLN A 734 ASN A 752 HIS ** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8992 Z= 0.365 Angle : 0.666 7.761 12222 Z= 0.354 Chirality : 0.048 0.150 1393 Planarity : 0.005 0.052 1555 Dihedral : 4.870 24.498 1204 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.98 % Allowed : 17.12 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.36 (0.24), residues: 1095 helix: -0.44 (0.22), residues: 522 sheet: -1.05 (0.42), residues: 121 loop : -1.27 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 162 HIS 0.011 0.002 HIS A 309 PHE 0.022 0.003 PHE A 165 TYR 0.027 0.003 TYR A 877 ARG 0.008 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7986 (m-80) cc_final: 0.7560 (m-80) REVERT: A 361 LEU cc_start: 0.7120 (mt) cc_final: 0.6836 (tt) REVERT: A 508 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8225 (mmtp) REVERT: A 553 ARG cc_start: 0.6419 (mmm-85) cc_final: 0.6156 (mtp85) REVERT: A 658 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6383 (mt-10) REVERT: A 811 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: B 155 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7022 (pm20) REVERT: B 176 ASN cc_start: 0.8475 (t0) cc_final: 0.7965 (t0) REVERT: C 8 CYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7471 (m) REVERT: C 62 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5561 (pmm) REVERT: D 93 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7379 (p) outliers start: 48 outliers final: 20 residues processed: 191 average time/residue: 1.0096 time to fit residues: 207.6863 Evaluate side-chains 159 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 0.0010 chunk 87 optimal weight: 0.0470 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 408 GLN A 416 ASN A 543 ASN A 752 HIS A 872 HIS B 118 ASN B 140 ASN B 158 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8992 Z= 0.135 Angle : 0.500 8.376 12222 Z= 0.266 Chirality : 0.041 0.134 1393 Planarity : 0.004 0.040 1555 Dihedral : 4.154 21.815 1204 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.32 % Allowed : 20.85 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.79 (0.25), residues: 1095 helix: 0.13 (0.23), residues: 518 sheet: -0.80 (0.42), residues: 121 loop : -1.10 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 182 HIS 0.003 0.001 HIS C 36 PHE 0.016 0.001 PHE A 415 TYR 0.018 0.001 TYR A 867 ARG 0.002 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7768 (m-80) cc_final: 0.7312 (m-80) REVERT: A 361 LEU cc_start: 0.7048 (mt) cc_final: 0.6796 (tt) REVERT: A 508 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8070 (mmtp) REVERT: A 553 ARG cc_start: 0.6295 (mmm-85) cc_final: 0.6059 (mtp85) REVERT: A 658 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6342 (mt-10) REVERT: B 165 LYS cc_start: 0.6504 (mtmm) cc_final: 0.6246 (mptm) REVERT: B 176 ASN cc_start: 0.8420 (t0) cc_final: 0.8053 (t160) REVERT: C 62 MET cc_start: 0.5740 (pmm) cc_final: 0.5505 (pmm) outliers start: 32 outliers final: 12 residues processed: 164 average time/residue: 0.9535 time to fit residues: 169.5492 Evaluate side-chains 154 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 543 ASN A 573 GLN A 613 HIS A 752 HIS A 872 HIS B 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8992 Z= 0.398 Angle : 0.637 10.275 12222 Z= 0.335 Chirality : 0.048 0.170 1393 Planarity : 0.005 0.049 1555 Dihedral : 4.702 22.275 1204 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.39 % Allowed : 19.71 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.17 (0.24), residues: 1095 helix: -0.17 (0.23), residues: 513 sheet: -0.93 (0.42), residues: 134 loop : -1.33 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 162 HIS 0.009 0.002 HIS A 309 PHE 0.018 0.003 PHE A 415 TYR 0.025 0.003 TYR A 289 ARG 0.005 0.001 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 138 time to evaluate : 0.945 Fit side-chains REVERT: A 334 PHE cc_start: 0.8021 (m-80) cc_final: 0.7583 (m-80) REVERT: A 361 LEU cc_start: 0.7147 (mt) cc_final: 0.6761 (tt) REVERT: A 508 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8209 (mmtp) REVERT: A 658 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6501 (mt-10) REVERT: A 811 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6638 (mm-30) REVERT: A 887 TYR cc_start: 0.7625 (t80) cc_final: 0.7362 (t80) REVERT: B 90 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6922 (ttt) REVERT: B 145 THR cc_start: 0.7978 (m) cc_final: 0.7718 (p) REVERT: B 176 ASN cc_start: 0.8581 (t0) cc_final: 0.8022 (t0) REVERT: B 179 ASN cc_start: 0.7471 (t0) cc_final: 0.7207 (t0) REVERT: B 180 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6583 (mm) REVERT: C 3 MET cc_start: 0.6629 (ttp) cc_final: 0.6426 (tpt) outliers start: 52 outliers final: 29 residues processed: 177 average time/residue: 1.0794 time to fit residues: 205.0292 Evaluate side-chains 169 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.0770 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN A 752 HIS A 872 HIS B 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8992 Z= 0.139 Angle : 0.500 9.980 12222 Z= 0.265 Chirality : 0.041 0.128 1393 Planarity : 0.003 0.037 1555 Dihedral : 4.170 19.775 1204 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.32 % Allowed : 22.61 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.69 (0.25), residues: 1095 helix: 0.30 (0.23), residues: 518 sheet: -0.67 (0.43), residues: 123 loop : -1.21 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 PHE 0.018 0.001 PHE A 415 TYR 0.015 0.001 TYR A 289 ARG 0.002 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.058 Fit side-chains REVERT: A 334 PHE cc_start: 0.7876 (m-80) cc_final: 0.7406 (m-80) REVERT: A 361 LEU cc_start: 0.7171 (mt) cc_final: 0.6770 (tt) REVERT: A 508 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8068 (mmtp) REVERT: A 658 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: A 811 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: B 90 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6696 (tmt) REVERT: B 145 THR cc_start: 0.7933 (m) cc_final: 0.7716 (p) REVERT: B 176 ASN cc_start: 0.8501 (t0) cc_final: 0.8122 (t160) REVERT: B 179 ASN cc_start: 0.7486 (t0) cc_final: 0.7277 (t0) REVERT: B 180 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6654 (mm) outliers start: 32 outliers final: 15 residues processed: 158 average time/residue: 1.0339 time to fit residues: 176.7426 Evaluate side-chains 151 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 416 ASN A 543 ASN A 600 ASN A 872 HIS B 158 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8992 Z= 0.271 Angle : 0.550 10.533 12222 Z= 0.292 Chirality : 0.044 0.130 1393 Planarity : 0.004 0.039 1555 Dihedral : 4.335 21.754 1204 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.36 % Allowed : 21.58 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.86 (0.25), residues: 1095 helix: 0.16 (0.23), residues: 513 sheet: -0.71 (0.44), residues: 123 loop : -1.30 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.010 0.001 HIS A 309 PHE 0.016 0.002 PHE A 415 TYR 0.021 0.002 TYR A 289 ARG 0.003 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 1.074 Fit side-chains REVERT: A 334 PHE cc_start: 0.7935 (m-80) cc_final: 0.7488 (m-80) REVERT: A 508 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8299 (mmtp) REVERT: A 658 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6521 (mt-10) REVERT: A 811 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6682 (mm-30) REVERT: A 887 TYR cc_start: 0.7644 (t80) cc_final: 0.7415 (t80) REVERT: B 90 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6774 (tmt) REVERT: B 145 THR cc_start: 0.7933 (m) cc_final: 0.7696 (p) REVERT: B 176 ASN cc_start: 0.8527 (t0) cc_final: 0.8090 (t0) REVERT: B 179 ASN cc_start: 0.7559 (t0) cc_final: 0.7343 (t0) REVERT: B 180 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6505 (mm) outliers start: 42 outliers final: 24 residues processed: 162 average time/residue: 1.0783 time to fit residues: 187.8063 Evaluate side-chains 163 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 543 ASN A 872 HIS B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8992 Z= 0.150 Angle : 0.493 10.759 12222 Z= 0.261 Chirality : 0.041 0.131 1393 Planarity : 0.003 0.034 1555 Dihedral : 4.078 19.012 1204 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.22 % Allowed : 22.72 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.57 (0.25), residues: 1095 helix: 0.43 (0.24), residues: 516 sheet: -0.42 (0.46), residues: 110 loop : -1.22 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.019 0.001 PHE A 415 TYR 0.013 0.001 TYR A 606 ARG 0.002 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.168 Fit side-chains REVERT: A 334 PHE cc_start: 0.7881 (m-80) cc_final: 0.7445 (m-80) REVERT: A 361 LEU cc_start: 0.7096 (mp) cc_final: 0.6776 (tp) REVERT: A 508 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8063 (mmtp) REVERT: A 658 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6484 (mt-10) REVERT: A 811 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6688 (mm-30) REVERT: B 90 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6736 (tmt) REVERT: B 145 THR cc_start: 0.7940 (m) cc_final: 0.7681 (p) REVERT: B 179 ASN cc_start: 0.7517 (t0) cc_final: 0.7316 (t0) REVERT: C 3 MET cc_start: 0.7234 (tpt) cc_final: 0.6871 (tpp) REVERT: C 35 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7298 (mt) outliers start: 31 outliers final: 18 residues processed: 160 average time/residue: 1.0508 time to fit residues: 181.4187 Evaluate side-chains 155 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 overall best weight: 2.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 543 ASN A 872 HIS B 118 ASN B 158 GLN B 176 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8992 Z= 0.221 Angle : 0.528 10.796 12222 Z= 0.281 Chirality : 0.043 0.127 1393 Planarity : 0.004 0.037 1555 Dihedral : 4.221 21.169 1204 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.42 % Allowed : 22.30 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.71 (0.25), residues: 1095 helix: 0.31 (0.23), residues: 517 sheet: -0.60 (0.44), residues: 123 loop : -1.27 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.008 0.001 HIS A 309 PHE 0.020 0.002 PHE A 415 TYR 0.025 0.002 TYR A 887 ARG 0.002 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 1.004 Fit side-chains REVERT: A 334 PHE cc_start: 0.7935 (m-80) cc_final: 0.7502 (m-80) REVERT: A 508 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8242 (mmtp) REVERT: A 658 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6458 (mt-10) REVERT: B 90 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6839 (tmt) REVERT: B 145 THR cc_start: 0.8053 (m) cc_final: 0.7796 (p) REVERT: C 3 MET cc_start: 0.7319 (tpt) cc_final: 0.7038 (tpp) outliers start: 33 outliers final: 21 residues processed: 157 average time/residue: 1.0974 time to fit residues: 185.1229 Evaluate side-chains 155 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 543 ASN A 872 HIS B 118 ASN B 158 GLN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8992 Z= 0.134 Angle : 0.490 10.437 12222 Z= 0.261 Chirality : 0.041 0.126 1393 Planarity : 0.003 0.034 1555 Dihedral : 4.001 18.291 1204 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.70 % Allowed : 23.65 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.44 (0.25), residues: 1095 helix: 0.52 (0.24), residues: 517 sheet: -0.26 (0.47), residues: 110 loop : -1.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.022 0.001 PHE A 415 TYR 0.016 0.001 TYR A 453 ARG 0.002 0.000 ARG A 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.996 Fit side-chains REVERT: A 334 PHE cc_start: 0.7847 (m-80) cc_final: 0.7427 (m-80) REVERT: A 494 ILE cc_start: 0.8453 (mm) cc_final: 0.8250 (mp) REVERT: A 508 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8049 (mmtp) REVERT: A 658 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: B 145 THR cc_start: 0.7947 (m) cc_final: 0.7717 (p) REVERT: C 3 MET cc_start: 0.7378 (tpt) cc_final: 0.7088 (tpp) outliers start: 26 outliers final: 20 residues processed: 158 average time/residue: 1.0193 time to fit residues: 173.8632 Evaluate side-chains 156 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 543 ASN A 872 HIS ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.184147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151144 restraints weight = 10096.200| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.90 r_work: 0.3531 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8992 Z= 0.205 Angle : 0.521 10.296 12222 Z= 0.277 Chirality : 0.042 0.127 1393 Planarity : 0.003 0.035 1555 Dihedral : 4.148 21.078 1204 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.80 % Allowed : 23.34 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.55 (0.25), residues: 1095 helix: 0.41 (0.24), residues: 511 sheet: -0.47 (0.46), residues: 123 loop : -1.14 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.009 0.001 HIS A 309 PHE 0.019 0.002 PHE A 415 TYR 0.017 0.002 TYR A 606 ARG 0.002 0.000 ARG A 651 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3627.11 seconds wall clock time: 65 minutes 4.97 seconds (3904.97 seconds total)