Starting phenix.real_space_refine on Wed Mar 20 04:27:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3p_31671/03_2024/7v3p_31671_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3p_31671/03_2024/7v3p_31671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3p_31671/03_2024/7v3p_31671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3p_31671/03_2024/7v3p_31671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3p_31671/03_2024/7v3p_31671_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3p_31671/03_2024/7v3p_31671_neut_trim.pdb" } resolution = 3.6 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= 0.003 sd= 0.047 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 S 101 5.16 5 C 8545 2.51 5 N 2330 2.21 5 O 2541 1.98 5 H 12814 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26331 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 12605 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 44, 'TRANS': 762} Chain breaks: 6 Chain: "B" Number of atoms: 12900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 12900 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 46, 'TRANS': 769} Chain breaks: 5 Chain: "E" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 299 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 471 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.83, per 1000 atoms: 0.45 Number of scatterers: 26331 At special positions: 0 Unit cell: (93.96, 116.64, 187.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 O 2541 8.00 N 2330 7.00 C 8545 6.00 H 12814 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.05 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 670 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=1.99 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.04 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.04 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS F 19 " 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 21 " " NAG A1002 " - " ASN A 387 " " NAG A1003 " - " ASN A 105 " " NAG B1001 " - " ASN B 504 " Time building additional restraints: 19.78 Conformation dependent library (CDL) restraints added in 2.7 seconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 38 sheets defined 15.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 Processing helix chain 'A' and resid 39 through 43 removed outlier: 4.012A pdb=" N TYR A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.761A pdb=" N CYS A 189 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 339 through 349 removed outlier: 4.066A pdb=" N GLU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.405A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.839A pdb=" N ILE A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.711A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 675 through 697 removed outlier: 4.049A pdb=" N ALA A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.642A pdb=" N GLN B 15 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 17 " --> pdb=" O GLN B 14 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 248 through 254 removed outlier: 3.935A pdb=" N CYS B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.889A pdb=" N GLU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 625 through 630 removed outlier: 4.010A pdb=" N ARG B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 630' Processing helix chain 'B' and resid 631 through 635 removed outlier: 3.986A pdb=" N LYS B 635 " --> pdb=" O TYR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.816A pdb=" N GLN B 680 " --> pdb=" O GLU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 12 through 20 removed outlier: 4.288A pdb=" N GLU E 17 " --> pdb=" O TYR E 14 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN E 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR E 19 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.252A pdb=" N LEU A 29 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 111 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL A 140 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE A 113 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 3.729A pdb=" N ILE A 76 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165 removed outlier: 3.927A pdb=" N THR A 165 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 172 " --> pdb=" O THR A 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.602A pdb=" N GLU A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 209 removed outlier: 3.850A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA8, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 267 through 269 removed outlier: 3.589A pdb=" N MET A 274 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB2, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AB3, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.900A pdb=" N LEU A 331 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA A 419 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 392 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 465 through 470 Processing sheet with id=AB5, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.973A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA A 567 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.973A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 585 through 590 removed outlier: 5.804A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.950A pdb=" N TYR A 613 " --> pdb=" O CYS A 776 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 773 " --> pdb=" O ASN A 789 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 775 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA A 787 " --> pdb=" O SER A 775 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 809 through 813 removed outlier: 3.834A pdb=" N ALA A 861 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.850A pdb=" N ILE A 837 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.850A pdb=" N ILE A 837 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AC4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.281A pdb=" N ILE B 7 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU B 32 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 164 through 167 removed outlier: 3.564A pdb=" N THR B 165 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 172 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 205 through 209 removed outlier: 3.531A pdb=" N ALA B 220 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AC8, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AC9, first strand: chain 'B' and resid 267 through 269 Processing sheet with id=AD1, first strand: chain 'B' and resid 281 through 282 removed outlier: 3.735A pdb=" N ILE B 282 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.636A pdb=" N LEU B 331 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ALA B 419 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 393 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD4, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AD5, first strand: chain 'B' and resid 465 through 470 Processing sheet with id=AD6, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.549A pdb=" N SER B 492 " --> pdb=" O VAL B 554 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.489A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 750 through 752 removed outlier: 3.928A pdb=" N TYR B 614 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 613 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 789 " --> pdb=" O ILE B 773 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AE1, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.823A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.823A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 858 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: 10.21 Time building geometry restraints manager: 20.79 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: 12803 1.02 - 1.22: 109 1.22 - 1.42: 5797 1.42 - 1.62: 7812 1.62 - 1.82: 126 Bond restraints: 26647 Sorted by residual: bond pdb=" CA TRP B 402 " pdb=" C TRP B 402 " ideal model delta sigma weight residual 1.526 1.415 0.112 1.21e-02 6.83e+03 8.55e+01 bond pdb=" CA VAL B 580 " pdb=" C VAL B 580 " ideal model delta sigma weight residual 1.524 1.438 0.087 1.05e-02 9.07e+03 6.80e+01 bond pdb=" CA SER B 579 " pdb=" C SER B 579 " ideal model delta sigma weight residual 1.527 1.418 0.109 1.42e-02 4.96e+03 5.87e+01 bond pdb=" CA SER B 288 " pdb=" C SER B 288 " ideal model delta sigma weight residual 1.529 1.424 0.105 1.40e-02 5.10e+03 5.63e+01 bond pdb=" CA LEU A 696 " pdb=" C LEU A 696 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.35e-02 5.49e+03 5.37e+01 ... (remaining 26642 not shown) Histogram of bond angle deviations from ideal: 81.75 - 92.78: 3 92.78 - 103.82: 258 103.82 - 114.85: 32489 114.85 - 125.88: 14793 125.88 - 136.91: 351 Bond angle restraints: 47894 Sorted by residual: angle pdb=" C ILE A 583 " pdb=" N PRO A 584 " pdb=" CA PRO A 584 " ideal model delta sigma weight residual 119.99 103.72 16.27 1.08e+00 8.57e-01 2.27e+02 angle pdb=" N ASN A 698 " pdb=" CA ASN A 698 " pdb=" C ASN A 698 " ideal model delta sigma weight residual 111.54 97.27 14.27 1.36e+00 5.41e-01 1.10e+02 angle pdb=" N ASN B 284 " pdb=" CA ASN B 284 " pdb=" C ASN B 284 " ideal model delta sigma weight residual 110.46 96.18 14.28 1.48e+00 4.57e-01 9.30e+01 angle pdb=" N LYS B 300 " pdb=" CA LYS B 300 " pdb=" C LYS B 300 " ideal model delta sigma weight residual 109.86 96.23 13.63 1.55e+00 4.16e-01 7.73e+01 angle pdb=" N ILE A 583 " pdb=" CA ILE A 583 " pdb=" C ILE A 583 " ideal model delta sigma weight residual 108.88 127.87 -18.99 2.16e+00 2.14e-01 7.73e+01 ... (remaining 47889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11469 17.92 - 35.85: 936 35.85 - 53.77: 294 53.77 - 71.70: 89 71.70 - 89.62: 34 Dihedral angle restraints: 12822 sinusoidal: 7002 harmonic: 5820 Sorted by residual: dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 22 " pdb=" CB CYS A 22 " ideal model delta sinusoidal sigma weight residual -86.00 -175.62 89.62 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS E 7 " pdb=" SG CYS E 7 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -174.67 88.67 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS B 294 " pdb=" SG CYS B 294 " pdb=" SG CYS B 298 " pdb=" CB CYS B 298 " ideal model delta sinusoidal sigma weight residual 93.00 176.62 -83.62 1 1.00e+01 1.00e-02 8.53e+01 ... (remaining 12819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 2023 0.292 - 0.584: 4 0.584 - 0.876: 0 0.876 - 1.168: 0 1.168 - 1.460: 1 Chirality restraints: 2028 Sorted by residual: chirality pdb=" CB THR B 675 " pdb=" CA THR B 675 " pdb=" OG1 THR B 675 " pdb=" CG2 THR B 675 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.33e+01 chirality pdb=" CA ASN B 11 " pdb=" N ASN B 11 " pdb=" C ASN B 11 " pdb=" CB ASN B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA PRO B 581 " pdb=" N PRO B 581 " pdb=" C PRO B 581 " pdb=" CB PRO B 581 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2025 not shown) Planarity restraints: 3972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 452 " 0.059 2.00e-02 2.50e+03 4.89e-01 3.59e+03 pdb=" CG ASN A 452 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 452 " -0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 452 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 452 " 0.844 2.00e-02 2.50e+03 pdb="HD22 ASN A 452 " -0.847 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 400 " 0.037 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN B 400 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN B 400 " -0.034 2.00e-02 2.50e+03 pdb=" NE2 GLN B 400 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 400 " 0.768 2.00e-02 2.50e+03 pdb="HE22 GLN B 400 " -0.761 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 608 " -0.059 2.00e-02 2.50e+03 4.40e-01 2.90e+03 pdb=" CG ASN A 608 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 608 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN A 608 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 608 " 0.758 2.00e-02 2.50e+03 pdb="HD22 ASN A 608 " -0.761 2.00e-02 2.50e+03 ... (remaining 3969 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1009 2.15 - 2.76: 49273 2.76 - 3.38: 70029 3.38 - 3.99: 89635 3.99 - 4.60: 139051 Nonbonded interactions: 348997 Sorted by model distance: nonbonded pdb=" O PRO B 71 " pdb="HD21 ASN B 102 " model vdw 1.539 1.850 nonbonded pdb=" O TYR B 628 " pdb="HE21 GLN B 853 " model vdw 1.551 1.850 nonbonded pdb=" O PRO B 584 " pdb="HD21 ASN B 789 " model vdw 1.569 1.850 nonbonded pdb="HE21 GLN B 680 " pdb=" OE2 GLU B 684 " model vdw 1.578 1.850 nonbonded pdb=" O ASN A 631 " pdb=" HG SER A 634 " model vdw 1.595 1.850 ... (remaining 348992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 37 or resid 41 through 154 or resid 162 through \ 424 or (resid 425 and (name N or name CA or name C or name O or name CB or name \ SG or name H or name HA or name HB2 or name HB3)) or resid 426 through 897 or re \ sid 1001)) selection = (chain 'B' and (resid 1 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3 or name HD21)) or resid 22 through 104 or (resid 105 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 106 thr \ ough 257 or resid 266 through 293 or resid 299 through 386 or (resid 387 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 388 throu \ gh 672 or (resid 673 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD )) or (resid 674 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ )) or (resid 675 and (name N \ or name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 6 \ 76 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name OE2)) or (resid 677 and (name N or name CA or name C or name \ O or name CB )) or (resid 678 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name OE2)) or (resid 679 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 680 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name OE1 or name NE2)) or (resid 681 and (name N or name CA \ or name C or name O or name CB )) or (resid 682 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid \ 683 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ )) or (resid 684 through 685 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (res \ id 686 and (name N or name CA or name C or name O or name CB )) or (resid 687 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e OE1 or name OE2)) or (resid 688 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or \ name OH )) or (resid 689 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid \ 690 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ )) or (resid 691 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 692 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or nam \ e CE2 or name CZ )) or (resid 693 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2)) or (resid 694 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) \ or (resid 695 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 696 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or (resid 697 and (name N or name CA or name C or name O or name CB or na \ me CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 698 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) \ or resid 699 through 704 or resid 744 through 897 or resid 1001)) } 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: 2.850 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: 0.430 Extract box with map and model: 8.040 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 81.470 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 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 : 0.008 0.112 13833 Z= 0.545 Angle : 1.136 18.985 18750 Z= 0.711 Chirality : 0.067 1.460 2028 Planarity : 0.008 0.106 2430 Dihedral : 14.313 89.506 5228 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.73 % Favored : 91.30 % Rotamer: Outliers : 2.27 % Allowed : 1.67 % Favored : 96.06 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1644 helix: -2.90 (0.36), residues: 151 sheet: -0.97 (0.26), residues: 383 loop : -1.50 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 176 HIS 0.010 0.001 HIS A 364 PHE 0.022 0.002 PHE A 45 TYR 0.038 0.002 TYR A 628 ARG 0.009 0.001 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 2.334 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: A 1 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.6016 (mt-10) REVERT: A 11 ASN cc_start: 0.6521 (OUTLIER) cc_final: 0.6033 (m-40) REVERT: A 700 ILE cc_start: 0.7402 (mt) cc_final: 0.7036 (tt) REVERT: B 139 ILE cc_start: 0.7923 (mp) cc_final: 0.7668 (mt) REVERT: B 403 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.4970 (t0) outliers start: 34 outliers final: 10 residues processed: 173 average time/residue: 0.5591 time to fit residues: 141.1865 Evaluate side-chains 112 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 0.0030 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN B 318 GLN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13833 Z= 0.206 Angle : 0.654 11.139 18750 Z= 0.357 Chirality : 0.056 1.384 2028 Planarity : 0.005 0.068 2430 Dihedral : 8.204 70.150 1968 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.30 % Favored : 92.52 % Rotamer: Outliers : 1.60 % Allowed : 5.94 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.20), residues: 1644 helix: -2.40 (0.36), residues: 158 sheet: -0.97 (0.26), residues: 370 loop : -1.27 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 618 HIS 0.006 0.001 HIS A 774 PHE 0.025 0.001 PHE A 701 TYR 0.026 0.002 TYR A 628 ARG 0.004 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 2.243 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: A 1 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5600 (mt-10) outliers start: 24 outliers final: 14 residues processed: 113 average time/residue: 0.4708 time to fit residues: 82.9269 Evaluate side-chains 102 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 125 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13833 Z= 0.170 Angle : 0.578 11.120 18750 Z= 0.310 Chirality : 0.055 1.378 2028 Planarity : 0.004 0.054 2430 Dihedral : 7.418 61.588 1963 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.87 % Favored : 92.94 % Rotamer: Outliers : 1.34 % Allowed : 7.34 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1644 helix: -2.05 (0.38), residues: 161 sheet: -1.09 (0.25), residues: 391 loop : -1.15 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 618 HIS 0.006 0.001 HIS A 774 PHE 0.015 0.001 PHE A 701 TYR 0.025 0.001 TYR A 628 ARG 0.004 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 2.162 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: A 1 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.5595 (mt-10) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.5183 time to fit residues: 86.1960 Evaluate side-chains 103 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13833 Z= 0.402 Angle : 0.714 11.186 18750 Z= 0.388 Chirality : 0.059 1.391 2028 Planarity : 0.006 0.054 2430 Dihedral : 7.853 62.450 1959 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.62 % Favored : 88.20 % Rotamer: Outliers : 1.80 % Allowed : 8.74 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.20), residues: 1644 helix: -2.44 (0.34), residues: 165 sheet: -1.41 (0.25), residues: 375 loop : -1.65 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 618 HIS 0.013 0.002 HIS B 774 PHE 0.024 0.002 PHE A 695 TYR 0.030 0.002 TYR B 391 ARG 0.006 0.001 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 2.098 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: A 1 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5600 (mt-10) REVERT: A 289 MET cc_start: 0.6680 (mpp) cc_final: 0.6093 (mtp) outliers start: 27 outliers final: 20 residues processed: 116 average time/residue: 0.4557 time to fit residues: 83.2040 Evaluate side-chains 115 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 802 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 0.0770 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13833 Z= 0.163 Angle : 0.577 11.239 18750 Z= 0.309 Chirality : 0.055 1.393 2028 Planarity : 0.004 0.050 2430 Dihedral : 7.286 64.229 1959 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.09 % Favored : 91.79 % Rotamer: Outliers : 1.00 % Allowed : 9.95 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.20), residues: 1644 helix: -2.00 (0.37), residues: 166 sheet: -1.34 (0.24), residues: 392 loop : -1.35 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 618 HIS 0.004 0.001 HIS B 774 PHE 0.012 0.001 PHE B 45 TYR 0.024 0.001 TYR A 628 ARG 0.003 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 2.378 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 289 MET cc_start: 0.6692 (mpp) cc_final: 0.6149 (mtp) outliers start: 15 outliers final: 10 residues processed: 116 average time/residue: 0.5640 time to fit residues: 95.8608 Evaluate side-chains 104 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13833 Z= 0.192 Angle : 0.567 11.190 18750 Z= 0.303 Chirality : 0.055 1.388 2028 Planarity : 0.004 0.049 2430 Dihedral : 6.924 63.149 1956 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.04 % Favored : 89.84 % Rotamer: Outliers : 1.20 % Allowed : 10.41 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1644 helix: -1.81 (0.39), residues: 166 sheet: -1.33 (0.24), residues: 387 loop : -1.30 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 544 HIS 0.005 0.001 HIS B 774 PHE 0.024 0.001 PHE A 45 TYR 0.023 0.001 TYR A 628 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 2.381 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 289 MET cc_start: 0.6760 (mpp) cc_final: 0.6278 (mtp) outliers start: 18 outliers final: 11 residues processed: 116 average time/residue: 0.5221 time to fit residues: 91.4523 Evaluate side-chains 109 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 802 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13833 Z= 0.215 Angle : 0.579 11.217 18750 Z= 0.310 Chirality : 0.056 1.394 2028 Planarity : 0.004 0.050 2430 Dihedral : 6.737 62.717 1952 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.85 % Favored : 90.02 % Rotamer: Outliers : 1.27 % Allowed : 11.21 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1644 helix: -1.63 (0.40), residues: 165 sheet: -1.40 (0.24), residues: 392 loop : -1.30 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 544 HIS 0.008 0.001 HIS B 774 PHE 0.032 0.002 PHE A 695 TYR 0.022 0.001 TYR A 628 ARG 0.006 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 2.034 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 11 ASN cc_start: 0.6266 (OUTLIER) cc_final: 0.6022 (m-40) REVERT: A 289 MET cc_start: 0.6771 (mpp) cc_final: 0.6343 (mtp) outliers start: 19 outliers final: 13 residues processed: 119 average time/residue: 0.5439 time to fit residues: 97.4336 Evaluate side-chains 114 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 802 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13833 Z= 0.183 Angle : 0.569 11.182 18750 Z= 0.304 Chirality : 0.056 1.389 2028 Planarity : 0.004 0.049 2430 Dihedral : 6.672 62.660 1952 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.31 % Favored : 90.51 % Rotamer: Outliers : 0.93 % Allowed : 11.68 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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 (0.21), residues: 1644 helix: -1.50 (0.40), residues: 165 sheet: -1.36 (0.24), residues: 396 loop : -1.26 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 544 HIS 0.006 0.001 HIS B 774 PHE 0.014 0.001 PHE F 24 TYR 0.022 0.001 TYR A 628 ARG 0.005 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.827 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: A 11 ASN cc_start: 0.6210 (OUTLIER) cc_final: 0.5993 (m-40) REVERT: A 289 MET cc_start: 0.6673 (mpp) cc_final: 0.6283 (mtp) outliers start: 14 outliers final: 11 residues processed: 116 average time/residue: 0.5390 time to fit residues: 93.5132 Evaluate side-chains 108 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 802 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.0060 chunk 117 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13833 Z= 0.153 Angle : 0.544 11.190 18750 Z= 0.289 Chirality : 0.055 1.391 2028 Planarity : 0.004 0.049 2430 Dihedral : 6.491 62.263 1952 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.79 % Favored : 92.03 % Rotamer: Outliers : 0.67 % Allowed : 12.08 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.84 (0.21), residues: 1644 helix: -1.29 (0.41), residues: 165 sheet: -1.27 (0.24), residues: 396 loop : -1.20 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 544 HIS 0.004 0.001 HIS B 774 PHE 0.012 0.001 PHE F 24 TYR 0.022 0.001 TYR A 628 ARG 0.004 0.000 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.998 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: A 289 MET cc_start: 0.6738 (mpp) cc_final: 0.6363 (mtp) REVERT: B 558 MET cc_start: 0.5802 (pp-130) cc_final: 0.5454 (ppp) outliers start: 10 outliers final: 9 residues processed: 108 average time/residue: 0.5367 time to fit residues: 87.1353 Evaluate side-chains 103 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 131 optimal weight: 0.2980 chunk 13 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 HIS ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13833 Z= 0.184 Angle : 0.551 11.235 18750 Z= 0.293 Chirality : 0.055 1.391 2028 Planarity : 0.004 0.048 2430 Dihedral : 6.494 60.873 1952 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.12 % Favored : 90.69 % Rotamer: Outliers : 0.87 % Allowed : 12.08 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.86 (0.21), residues: 1644 helix: -1.26 (0.42), residues: 165 sheet: -1.23 (0.25), residues: 382 loop : -1.26 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 544 HIS 0.006 0.001 HIS B 774 PHE 0.016 0.001 PHE F 24 TYR 0.022 0.001 TYR A 628 ARG 0.009 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 2.243 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: A 11 ASN cc_start: 0.6044 (OUTLIER) cc_final: 0.5811 (m-40) REVERT: A 289 MET cc_start: 0.6733 (mpp) cc_final: 0.6383 (mtp) outliers start: 13 outliers final: 12 residues processed: 106 average time/residue: 0.5258 time to fit residues: 84.5625 Evaluate side-chains 104 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 55 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.161061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121075 restraints weight = 74488.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126786 restraints weight = 44030.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128455 restraints weight = 28522.087| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13833 Z= 0.142 Angle : 0.531 11.194 18750 Z= 0.282 Chirality : 0.055 1.390 2028 Planarity : 0.004 0.043 2430 Dihedral : 6.354 60.735 1952 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.18 % Favored : 92.64 % Rotamer: Outliers : 0.53 % Allowed : 12.48 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.74 (0.21), residues: 1644 helix: -1.13 (0.42), residues: 165 sheet: -1.16 (0.25), residues: 386 loop : -1.16 (0.20), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 544 HIS 0.003 0.001 HIS A 774 PHE 0.016 0.001 PHE B 747 TYR 0.022 0.001 TYR A 628 ARG 0.005 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4729.00 seconds wall clock time: 84 minutes 31.03 seconds (5071.03 seconds total)