Starting phenix.real_space_refine on Thu Feb 15 14:16:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysh_34075/02_2024/7ysh_34075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysh_34075/02_2024/7ysh_34075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysh_34075/02_2024/7ysh_34075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysh_34075/02_2024/7ysh_34075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysh_34075/02_2024/7ysh_34075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ysh_34075/02_2024/7ysh_34075_updated.pdb" } resolution = 2.74 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= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 S 68 5.16 5 C 7979 2.51 5 N 2132 2.21 5 O 2299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 426": "OD1" <-> "OD2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A ASP 535": "OD1" <-> "OD2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A ASP 815": "OD1" <-> "OD2" Residue "A ARG 853": "NH1" <-> "NH2" Residue "A TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 865": "OD1" <-> "OD2" Residue "A ASP 884": "OD1" <-> "OD2" Residue "A TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A GLU 965": "OE1" <-> "OE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D ARG 209": "NH1" <-> "NH2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ASP 200": "OD1" <-> "OD2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12480 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7527 Classifications: {'peptide': 921} Link IDs: {'PTRANS': 51, 'TRANS': 869} Chain breaks: 1 Chain: "B" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1442 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 16, 'TRANS': 162} Chain: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1679 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 196} Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 195} Chain: "F" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {'IDS': 4, 'SGN': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5570 SG CYS A 739 44.956 47.129 41.364 1.00 40.63 S Time building chain proxies: 6.73, per 1000 atoms: 0.54 Number of scatterers: 12480 At special positions: 0 Unit cell: (87.68, 129.328, 147.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 68 16.00 O 2299 8.00 N 2132 7.00 C 7979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 963 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 621 " distance=2.02 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 970 " distance=2.04 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 113 " distance=2.03 Simple disulfide: pdb=" SG CYS D 178 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 341 " distance=2.03 Simple disulfide: pdb=" SG CYS E 178 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 341 " distance=2.02 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=4, symmetry=0 Links applied ALPHA1-4 " IDS F 2 " - " SGN F 3 " " IDS F 4 " - " SGN F 5 " " IDS F 6 " - " SGN F 7 " " IDS F 8 " - " SGN F 9 " BETA1-4 " SGN F 1 " - " IDS F 2 " ~> Even though IDS is an alpha isomer, a beta linkage is required... " SGN F 3 " - " IDS F 4 " " SGN F 5 " - " IDS F 6 " " SGN F 7 " - " IDS F 8 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 739 " 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 20 sheets defined 24.3% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 41 through 44 No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 51 through 54 No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 90 through 93 No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 325 through 332 Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 576 through 587 Proline residue: A 580 - end of helix Processing helix chain 'A' and resid 599 through 602 No H-bonds generated for 'chain 'A' and resid 599 through 602' Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 613 through 627 Processing helix chain 'A' and resid 649 through 652 No H-bonds generated for 'chain 'A' and resid 649 through 652' Processing helix chain 'A' and resid 660 through 679 removed outlier: 5.066A pdb=" N HIS A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 717 Processing helix chain 'A' and resid 719 through 722 No H-bonds generated for 'chain 'A' and resid 719 through 722' Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 758 through 764 Proline residue: A 763 - end of helix Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 791 through 797 Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.705A pdb=" N LYS A 862 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 863 " --> pdb=" O LYS A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 903 removed outlier: 3.540A pdb=" N LEU A 886 " --> pdb=" O GLU A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 949 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.510A pdb=" N MET D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing sheet with id= A, first strand: chain 'A' and resid 186 through 190 removed outlier: 7.030A pdb=" N ILE A 412 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR A 455 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU A 414 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 457 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE A 367 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 413 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 369 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN A 415 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 371 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 233 through 235 removed outlier: 6.156A pdb=" N GLN A 293 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 302 through 304 removed outlier: 3.699A pdb=" N TRP A 302 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 632 through 636 removed outlier: 4.002A pdb=" N SER A 596 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 870 " --> pdb=" O CYS A 910 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR A 912 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER A 872 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 914 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 804 " --> pdb=" O TYR A 869 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 871 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 806 " --> pdb=" O ILE A 871 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.477A pdb=" N LYS A 725 " --> pdb=" O TRP A 684 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 734 through 737 Processing sheet with id= G, first strand: chain 'A' and resid 928 through 931 Processing sheet with id= H, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.034A pdb=" N VAL A 563 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU A 548 " --> pdb=" O ASP A 561 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ASP A 561 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 157 through 161 removed outlier: 12.636A pdb=" N ILE B 40 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ILE B 55 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU B 42 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 93 through 96 Processing sheet with id= K, first strand: chain 'B' and resid 115 through 119 Processing sheet with id= L, first strand: chain 'B' and resid 75 through 79 removed outlier: 6.959A pdb=" N PHE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 165 through 169 removed outlier: 8.296A pdb=" N HIS D 166 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN D 244 " --> pdb=" O HIS D 166 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL D 168 " --> pdb=" O GLN D 244 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP D 246 " --> pdb=" O VAL D 168 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 174 through 177 Processing sheet with id= O, first strand: chain 'D' and resid 265 through 267 removed outlier: 4.926A pdb=" N GLU D 338 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS D 291 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE D 310 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 272 through 276 Processing sheet with id= Q, first strand: chain 'E' and resid 165 through 169 removed outlier: 8.638A pdb=" N HIS E 166 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN E 244 " --> pdb=" O HIS E 166 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL E 168 " --> pdb=" O GLN E 244 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP E 246 " --> pdb=" O VAL E 168 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 174 through 177 Processing sheet with id= S, first strand: chain 'E' and resid 286 through 288 Processing sheet with id= T, first strand: chain 'E' and resid 338 through 340 348 hydrogen bonds defined for protein. 945 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: 3.68 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1967 1.25 - 1.39: 3422 1.39 - 1.54: 7133 1.54 - 1.68: 252 1.68 - 1.82: 86 Bond restraints: 12860 Sorted by residual: bond pdb=" C SER D 219 " pdb=" O SER D 219 " ideal model delta sigma weight residual 1.235 1.109 0.126 1.26e-02 6.30e+03 1.00e+02 bond pdb=" C LEU B 39 " pdb=" O LEU B 39 " ideal model delta sigma weight residual 1.235 1.150 0.085 1.20e-02 6.94e+03 4.99e+01 bond pdb=" C SER E 223 " pdb=" O SER E 223 " ideal model delta sigma weight residual 1.235 1.147 0.088 1.38e-02 5.25e+03 4.05e+01 bond pdb=" O2 IDS F 2 " pdb=" S IDS F 2 " ideal model delta sigma weight residual 1.646 1.524 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" O2 IDS F 8 " pdb=" S IDS F 8 " ideal model delta sigma weight residual 1.646 1.526 0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 12855 not shown) Histogram of bond angle deviations from ideal: 78.87 - 91.42: 2 91.42 - 103.97: 257 103.97 - 116.51: 8607 116.51 - 129.06: 8489 129.06 - 141.61: 166 Bond angle restraints: 17521 Sorted by residual: angle pdb=" C5 SGN F 1 " pdb=" C4 SGN F 1 " pdb=" O4 SGN F 1 " ideal model delta sigma weight residual 108.84 78.87 29.97 3.00e+00 1.11e-01 9.98e+01 angle pdb=" C5 IDS F 2 " pdb=" C4 IDS F 2 " pdb=" O4 IDS F 2 " ideal model delta sigma weight residual 113.47 141.61 -28.14 3.00e+00 1.11e-01 8.80e+01 angle pdb=" C5 SGN F 7 " pdb=" C4 SGN F 7 " pdb=" O4 SGN F 7 " ideal model delta sigma weight residual 108.84 136.63 -27.79 3.00e+00 1.11e-01 8.58e+01 angle pdb=" C3 SGN F 3 " pdb=" C4 SGN F 3 " pdb=" O4 SGN F 3 " ideal model delta sigma weight residual 108.83 134.64 -25.81 3.00e+00 1.11e-01 7.40e+01 angle pdb=" C3 SGN F 1 " pdb=" C4 SGN F 1 " pdb=" O4 SGN F 1 " ideal model delta sigma weight residual 108.83 86.55 22.28 3.00e+00 1.11e-01 5.52e+01 ... (remaining 17516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.32: 7166 25.32 - 50.64: 386 50.64 - 75.97: 50 75.97 - 101.29: 32 101.29 - 126.61: 63 Dihedral angle restraints: 7697 sinusoidal: 3255 harmonic: 4442 Sorted by residual: dihedral pdb=" CB CYS A 910 " pdb=" SG CYS A 910 " pdb=" SG CYS A 970 " pdb=" CB CYS A 970 " ideal model delta sinusoidal sigma weight residual -86.00 -154.13 68.13 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CA LEU A 253 " pdb=" C LEU A 253 " pdb=" N ALA A 254 " pdb=" CA ALA A 254 " ideal model delta harmonic sigma weight residual 180.00 -142.28 -37.72 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA LYS A 555 " pdb=" C LYS A 555 " pdb=" N ARG A 556 " pdb=" CA ARG A 556 " ideal model delta harmonic sigma weight residual 180.00 146.49 33.51 0 5.00e+00 4.00e-02 4.49e+01 ... (remaining 7694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 1826 0.223 - 0.447: 22 0.447 - 0.670: 1 0.670 - 0.893: 3 0.893 - 1.117: 3 Chirality restraints: 1855 Sorted by residual: chirality pdb=" C1 IDS F 6 " pdb=" O4 SGN F 5 " pdb=" C2 IDS F 6 " pdb=" O5 IDS F 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.76e+02 chirality pdb=" C1 IDS F 8 " pdb=" O4 SGN F 7 " pdb=" C2 IDS F 8 " pdb=" O5 IDS F 8 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.33e+02 chirality pdb=" C1 IDS F 4 " pdb=" O4 SGN F 3 " pdb=" C2 IDS F 4 " pdb=" O5 IDS F 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.15e+02 ... (remaining 1852 not shown) Planarity restraints: 2234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 219 " -0.020 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C SER D 219 " 0.074 2.00e-02 2.50e+03 pdb=" O SER D 219 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL D 220 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 222 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C PRO E 222 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO E 222 " 0.024 2.00e-02 2.50e+03 pdb=" N SER E 223 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 459 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C SER A 459 " -0.064 2.00e-02 2.50e+03 pdb=" O SER A 459 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU A 460 " 0.021 2.00e-02 2.50e+03 ... (remaining 2231 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 67 2.47 - 3.08: 7598 3.08 - 3.68: 19579 3.68 - 4.29: 30309 4.29 - 4.90: 50057 Nonbonded interactions: 107610 Sorted by model distance: nonbonded pdb=" OE1 GLU B 121 " pdb=" OG SER E 223 " model vdw 1.859 2.440 nonbonded pdb=" NZ LYS E 177 " pdb=" OG1 THR E 212 " model vdw 1.956 2.520 nonbonded pdb=" OD1 ASP A 426 " pdb="ZN ZN A1001 " model vdw 2.081 2.230 nonbonded pdb=" CE LYS E 177 " pdb=" OG1 THR E 212 " model vdw 2.087 3.440 nonbonded pdb=" OD1 ASP A 815 " pdb="ZN ZN A1001 " model vdw 2.089 2.230 ... (remaining 107605 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 'D' and resid 148 through 359) selection = chain 'E' } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 36.530 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.010 0.126 12860 Z= 0.650 Angle : 1.214 29.972 17521 Z= 0.604 Chirality : 0.084 1.117 1855 Planarity : 0.008 0.072 2234 Dihedral : 20.562 126.608 4825 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.99 % Favored : 91.55 % Rotamer: Outliers : 1.06 % Allowed : 6.05 % Favored : 92.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.18), residues: 1515 helix: -2.44 (0.20), residues: 373 sheet: -1.40 (0.26), residues: 336 loop : -2.79 (0.18), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 458 HIS 0.006 0.001 HIS A 269 PHE 0.017 0.002 PHE A 595 TYR 0.027 0.003 TYR E 206 ARG 0.013 0.001 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 1.414 Fit side-chains REVERT: A 175 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7519 (mtm110) REVERT: A 230 GLN cc_start: 0.8297 (tp40) cc_final: 0.8075 (tm-30) REVERT: A 533 GLN cc_start: 0.6680 (mm-40) cc_final: 0.5779 (tt0) REVERT: A 653 ARG cc_start: 0.7051 (ttp-110) cc_final: 0.6829 (mtm-85) REVERT: A 772 TRP cc_start: 0.8164 (t-100) cc_final: 0.7873 (t-100) REVERT: A 774 MET cc_start: 0.8985 (ttt) cc_final: 0.8712 (ttt) REVERT: A 829 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7295 (mm-30) REVERT: A 868 MET cc_start: 0.9081 (mtt) cc_final: 0.8833 (mtt) REVERT: B 48 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6784 (tpp80) REVERT: B 70 TYR cc_start: 0.8408 (m-80) cc_final: 0.8092 (m-80) REVERT: B 75 ILE cc_start: 0.8623 (mt) cc_final: 0.8361 (mm) REVERT: B 109 ASP cc_start: 0.6937 (t70) cc_final: 0.6547 (t70) REVERT: B 118 GLN cc_start: 0.7530 (mt0) cc_final: 0.7236 (tt0) REVERT: B 199 MET cc_start: 0.7736 (ttm) cc_final: 0.7329 (ttm) REVERT: D 198 LYS cc_start: 0.8444 (pttp) cc_final: 0.7836 (ptpp) REVERT: D 321 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7697 (mmmt) REVERT: E 250 ARG cc_start: 0.8087 (ptt-90) cc_final: 0.7850 (ptt180) REVERT: E 280 TYR cc_start: 0.7875 (m-80) cc_final: 0.7563 (m-80) outliers start: 14 outliers final: 8 residues processed: 191 average time/residue: 1.3967 time to fit residues: 288.4137 Evaluate side-chains 145 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 359 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 130 ASN A 166 ASN A 186 GLN A 193 HIS A 198 GLN A 201 GLN A 290 GLN A 344 ASN A 378 GLN A 406 ASN A 530 ASN A 608 GLN A 610 GLN A 722 GLN A 779 ASN A 831 GLN A 857 ASN B 27 ASN B 131 GLN B 156 GLN B 168 HIS B 179 GLN D 244 GLN D 296 ASN D 309 GLN E 292 HIS E 296 ASN E 304 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12860 Z= 0.202 Angle : 0.673 9.341 17521 Z= 0.334 Chirality : 0.048 0.325 1855 Planarity : 0.006 0.131 2234 Dihedral : 21.043 166.340 1895 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.67 % Favored : 93.07 % Rotamer: Outliers : 1.97 % Allowed : 11.57 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1515 helix: -0.91 (0.24), residues: 384 sheet: -1.16 (0.27), residues: 341 loop : -2.27 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 466 HIS 0.005 0.001 HIS A 269 PHE 0.009 0.001 PHE D 176 TYR 0.013 0.001 TYR A 890 ARG 0.033 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7557 (mtm110) REVERT: A 204 TYR cc_start: 0.8595 (m-80) cc_final: 0.8199 (m-80) REVERT: A 533 GLN cc_start: 0.6622 (mm-40) cc_final: 0.5659 (tt0) REVERT: A 653 ARG cc_start: 0.7010 (ttp-110) cc_final: 0.6796 (mtm-85) REVERT: A 772 TRP cc_start: 0.8316 (t-100) cc_final: 0.7939 (t-100) REVERT: A 774 MET cc_start: 0.8868 (ttt) cc_final: 0.8528 (ttt) REVERT: A 829 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7227 (mm-30) REVERT: A 868 MET cc_start: 0.9060 (mtt) cc_final: 0.8792 (mtt) REVERT: A 934 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6790 (mp-120) REVERT: B 27 ASN cc_start: 0.4110 (OUTLIER) cc_final: 0.3837 (t0) REVERT: B 51 TYR cc_start: 0.7325 (m-80) cc_final: 0.6804 (m-80) REVERT: B 70 TYR cc_start: 0.8409 (m-80) cc_final: 0.8173 (m-80) REVERT: B 75 ILE cc_start: 0.8636 (mt) cc_final: 0.8385 (mm) REVERT: B 89 MET cc_start: 0.8681 (mmm) cc_final: 0.8378 (tpt) REVERT: B 109 ASP cc_start: 0.6805 (t70) cc_final: 0.6444 (t0) REVERT: B 118 GLN cc_start: 0.7495 (mt0) cc_final: 0.7261 (tt0) REVERT: B 199 MET cc_start: 0.7669 (ttm) cc_final: 0.7312 (ttm) REVERT: D 198 LYS cc_start: 0.8369 (pttp) cc_final: 0.8071 (mtmp) REVERT: D 276 MET cc_start: 0.7360 (tpp) cc_final: 0.7115 (mmt) REVERT: E 250 ARG cc_start: 0.8071 (ptt-90) cc_final: 0.7828 (ptt180) REVERT: E 280 TYR cc_start: 0.7829 (m-80) cc_final: 0.7531 (m-80) outliers start: 26 outliers final: 8 residues processed: 165 average time/residue: 1.3827 time to fit residues: 247.7370 Evaluate side-chains 142 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 203 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 HIS A 892 GLN B 27 ASN D 309 GLN D 351 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12860 Z= 0.386 Angle : 0.735 8.739 17521 Z= 0.365 Chirality : 0.052 0.321 1855 Planarity : 0.006 0.094 2234 Dihedral : 18.975 170.840 1891 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.99 % Favored : 91.75 % Rotamer: Outliers : 1.82 % Allowed : 13.24 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.10 (0.20), residues: 1515 helix: -0.51 (0.25), residues: 384 sheet: -1.01 (0.27), residues: 351 loop : -2.04 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 466 HIS 0.005 0.001 HIS A 592 PHE 0.014 0.002 PHE A 595 TYR 0.024 0.002 TYR A 432 ARG 0.030 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7561 (mtm110) REVERT: A 533 GLN cc_start: 0.6773 (mm-40) cc_final: 0.5907 (tt0) REVERT: A 653 ARG cc_start: 0.7097 (ttp-110) cc_final: 0.6836 (mtm-85) REVERT: A 772 TRP cc_start: 0.8371 (t-100) cc_final: 0.8006 (t-100) REVERT: A 774 MET cc_start: 0.8996 (ttt) cc_final: 0.8670 (ttt) REVERT: A 868 MET cc_start: 0.9093 (mtt) cc_final: 0.8884 (mtt) REVERT: A 934 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7007 (mt0) REVERT: B 51 TYR cc_start: 0.7345 (m-80) cc_final: 0.6934 (m-80) REVERT: B 89 MET cc_start: 0.8709 (mmm) cc_final: 0.8398 (tpt) REVERT: B 91 ARG cc_start: 0.7492 (mpp80) cc_final: 0.7068 (mtt90) REVERT: B 109 ASP cc_start: 0.6921 (t70) cc_final: 0.6557 (t0) REVERT: B 118 GLN cc_start: 0.7525 (mt0) cc_final: 0.7220 (tt0) REVERT: D 198 LYS cc_start: 0.8131 (pttp) cc_final: 0.7873 (mtmp) REVERT: E 250 ARG cc_start: 0.8069 (ptt-90) cc_final: 0.7807 (ptt180) REVERT: E 280 TYR cc_start: 0.7853 (m-80) cc_final: 0.7540 (m-80) outliers start: 24 outliers final: 13 residues processed: 147 average time/residue: 1.3324 time to fit residues: 212.9167 Evaluate side-chains 141 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain D residue 239 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 7.9990 chunk 103 optimal weight: 0.0770 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN D 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12860 Z= 0.271 Angle : 0.671 9.343 17521 Z= 0.333 Chirality : 0.050 0.290 1855 Planarity : 0.005 0.132 2234 Dihedral : 16.930 165.269 1889 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.00 % Favored : 92.74 % Rotamer: Outliers : 2.57 % Allowed : 13.62 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1515 helix: -0.10 (0.26), residues: 384 sheet: -0.81 (0.28), residues: 342 loop : -1.87 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 466 HIS 0.004 0.001 HIS A 269 PHE 0.010 0.001 PHE A 405 TYR 0.017 0.002 TYR A 432 ARG 0.025 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7526 (mtm110) REVERT: A 531 TYR cc_start: 0.7472 (m-80) cc_final: 0.7103 (m-80) REVERT: A 533 GLN cc_start: 0.6711 (mm-40) cc_final: 0.5864 (tt0) REVERT: A 653 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6826 (mtm-85) REVERT: A 772 TRP cc_start: 0.8342 (t-100) cc_final: 0.7950 (t-100) REVERT: A 774 MET cc_start: 0.8949 (ttt) cc_final: 0.8563 (ttt) REVERT: A 868 MET cc_start: 0.9057 (mtt) cc_final: 0.8789 (mtt) REVERT: A 934 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.6560 (mp-120) REVERT: B 51 TYR cc_start: 0.7229 (m-80) cc_final: 0.6848 (m-80) REVERT: B 57 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7799 (mtpp) REVERT: B 75 ILE cc_start: 0.8671 (mt) cc_final: 0.8374 (mm) REVERT: B 89 MET cc_start: 0.8715 (mmm) cc_final: 0.8360 (tpt) REVERT: B 91 ARG cc_start: 0.7452 (mpp80) cc_final: 0.7045 (mtt90) REVERT: B 109 ASP cc_start: 0.6949 (t70) cc_final: 0.6548 (t0) REVERT: D 198 LYS cc_start: 0.8104 (pttp) cc_final: 0.7660 (ptpp) REVERT: E 188 LEU cc_start: 0.4048 (OUTLIER) cc_final: 0.3777 (tp) REVERT: E 250 ARG cc_start: 0.8044 (ptt-90) cc_final: 0.7751 (ptt180) REVERT: E 280 TYR cc_start: 0.7862 (m-80) cc_final: 0.7535 (m-80) outliers start: 34 outliers final: 16 residues processed: 159 average time/residue: 1.2687 time to fit residues: 220.8368 Evaluate side-chains 147 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 108 optimal weight: 0.0770 chunk 60 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN D 309 GLN ** E 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12860 Z= 0.180 Angle : 0.637 8.351 17521 Z= 0.315 Chirality : 0.048 0.413 1855 Planarity : 0.008 0.310 2234 Dihedral : 16.144 141.047 1889 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.00 % Favored : 92.74 % Rotamer: Outliers : 2.34 % Allowed : 14.37 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.51 (0.21), residues: 1515 helix: 0.19 (0.27), residues: 384 sheet: -0.77 (0.28), residues: 344 loop : -1.73 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 466 HIS 0.005 0.001 HIS A 269 PHE 0.009 0.001 PHE A 595 TYR 0.026 0.001 TYR D 307 ARG 0.024 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.396 Fit side-chains REVERT: A 175 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7488 (mtm110) REVERT: A 533 GLN cc_start: 0.6697 (mm-40) cc_final: 0.5825 (tt0) REVERT: A 653 ARG cc_start: 0.6978 (ttp-110) cc_final: 0.6748 (mtm-85) REVERT: A 772 TRP cc_start: 0.8331 (t-100) cc_final: 0.7992 (t-100) REVERT: A 868 MET cc_start: 0.9033 (mtt) cc_final: 0.8737 (mtt) REVERT: A 934 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6760 (mp-120) REVERT: B 51 TYR cc_start: 0.7172 (m-80) cc_final: 0.6863 (m-80) REVERT: B 57 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7697 (mtpp) REVERT: B 75 ILE cc_start: 0.8630 (mt) cc_final: 0.8354 (mm) REVERT: B 89 MET cc_start: 0.8700 (mmm) cc_final: 0.8343 (tpt) REVERT: B 109 ASP cc_start: 0.6958 (t70) cc_final: 0.6571 (t0) REVERT: D 198 LYS cc_start: 0.8047 (pttp) cc_final: 0.7834 (mtmp) REVERT: E 188 LEU cc_start: 0.4087 (OUTLIER) cc_final: 0.3872 (tp) REVERT: E 280 TYR cc_start: 0.7875 (m-80) cc_final: 0.7584 (m-80) outliers start: 31 outliers final: 14 residues processed: 160 average time/residue: 1.2260 time to fit residues: 214.3475 Evaluate side-chains 146 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN B 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12860 Z= 0.307 Angle : 0.677 8.709 17521 Z= 0.337 Chirality : 0.050 0.338 1855 Planarity : 0.005 0.048 2234 Dihedral : 15.617 175.580 1887 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.46 % Favored : 92.28 % Rotamer: Outliers : 2.34 % Allowed : 15.20 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.49 (0.21), residues: 1515 helix: 0.12 (0.26), residues: 385 sheet: -0.71 (0.28), residues: 332 loop : -1.69 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 466 HIS 0.006 0.001 HIS E 351 PHE 0.012 0.002 PHE A 405 TYR 0.020 0.002 TYR A 432 ARG 0.009 0.001 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.231 Fit side-chains REVERT: A 175 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7506 (mtm110) REVERT: A 502 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: A 533 GLN cc_start: 0.6688 (mm-40) cc_final: 0.5915 (tt0) REVERT: A 653 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6816 (mtm-85) REVERT: A 772 TRP cc_start: 0.8362 (t-100) cc_final: 0.8026 (t-100) REVERT: A 868 MET cc_start: 0.9064 (mtt) cc_final: 0.8798 (mtt) REVERT: A 934 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.6522 (mp-120) REVERT: B 51 TYR cc_start: 0.7130 (m-80) cc_final: 0.6864 (m-80) REVERT: B 68 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7893 (p) REVERT: B 75 ILE cc_start: 0.8692 (mt) cc_final: 0.8397 (mm) REVERT: B 89 MET cc_start: 0.8712 (mmm) cc_final: 0.8407 (tpt) REVERT: B 109 ASP cc_start: 0.6943 (t70) cc_final: 0.6536 (t0) REVERT: D 198 LYS cc_start: 0.8016 (pttp) cc_final: 0.7796 (mtmp) REVERT: E 188 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3861 (tt) REVERT: E 280 TYR cc_start: 0.7915 (m-80) cc_final: 0.7623 (m-80) outliers start: 31 outliers final: 18 residues processed: 156 average time/residue: 1.2947 time to fit residues: 219.9174 Evaluate side-chains 149 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12860 Z= 0.236 Angle : 0.650 10.551 17521 Z= 0.321 Chirality : 0.048 0.352 1855 Planarity : 0.004 0.050 2234 Dihedral : 15.138 178.609 1887 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.19 % Favored : 92.54 % Rotamer: Outliers : 2.34 % Allowed : 15.66 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.37 (0.21), residues: 1515 helix: 0.27 (0.27), residues: 385 sheet: -0.68 (0.28), residues: 332 loop : -1.62 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 466 HIS 0.006 0.001 HIS E 351 PHE 0.009 0.001 PHE A 595 TYR 0.023 0.001 TYR D 307 ARG 0.012 0.001 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.448 Fit side-chains REVERT: A 175 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7507 (mtm110) REVERT: A 502 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: A 533 GLN cc_start: 0.6625 (mm-40) cc_final: 0.5884 (tt0) REVERT: A 653 ARG cc_start: 0.7018 (ttp-110) cc_final: 0.6779 (mtm-85) REVERT: A 772 TRP cc_start: 0.8358 (t-100) cc_final: 0.7993 (t-100) REVERT: A 868 MET cc_start: 0.9039 (mtt) cc_final: 0.8758 (mtt) REVERT: A 934 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.6553 (mp-120) REVERT: B 51 TYR cc_start: 0.7049 (m-80) cc_final: 0.6824 (m-80) REVERT: B 68 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7873 (p) REVERT: B 75 ILE cc_start: 0.8655 (mt) cc_final: 0.8359 (mm) REVERT: B 89 MET cc_start: 0.8687 (mmm) cc_final: 0.8416 (tpt) REVERT: B 109 ASP cc_start: 0.7021 (t70) cc_final: 0.6099 (t0) REVERT: B 149 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6680 (mpt) REVERT: D 198 LYS cc_start: 0.7992 (pttp) cc_final: 0.7779 (mtmp) REVERT: E 188 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.3908 (tt) REVERT: E 280 TYR cc_start: 0.7846 (m-80) cc_final: 0.7530 (m-80) outliers start: 31 outliers final: 18 residues processed: 153 average time/residue: 1.2823 time to fit residues: 215.3578 Evaluate side-chains 152 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12860 Z= 0.258 Angle : 0.652 8.506 17521 Z= 0.323 Chirality : 0.049 0.367 1855 Planarity : 0.005 0.056 2234 Dihedral : 14.571 177.457 1887 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.39 % Favored : 92.34 % Rotamer: Outliers : 2.34 % Allowed : 15.96 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.29 (0.21), residues: 1515 helix: 0.39 (0.27), residues: 379 sheet: -0.58 (0.29), residues: 328 loop : -1.61 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 466 HIS 0.005 0.001 HIS E 351 PHE 0.017 0.001 PHE A 917 TYR 0.017 0.002 TYR A 432 ARG 0.013 0.000 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.384 Fit side-chains REVERT: A 175 ARG cc_start: 0.7737 (ttp-110) cc_final: 0.7491 (mtm110) REVERT: A 502 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: A 531 TYR cc_start: 0.7634 (m-80) cc_final: 0.7270 (m-80) REVERT: A 533 GLN cc_start: 0.6681 (mm-40) cc_final: 0.5952 (tt0) REVERT: A 650 LEU cc_start: 0.8841 (tp) cc_final: 0.8596 (tp) REVERT: A 653 ARG cc_start: 0.7031 (ttp-110) cc_final: 0.6784 (mtm-85) REVERT: A 772 TRP cc_start: 0.8362 (t-100) cc_final: 0.7999 (t-100) REVERT: A 868 MET cc_start: 0.9042 (mtt) cc_final: 0.8760 (mtt) REVERT: A 934 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.6487 (mp-120) REVERT: B 51 TYR cc_start: 0.7027 (m-80) cc_final: 0.6813 (m-80) REVERT: B 68 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7956 (p) REVERT: B 75 ILE cc_start: 0.8663 (mt) cc_final: 0.8361 (mm) REVERT: B 89 MET cc_start: 0.8692 (mmm) cc_final: 0.8417 (tpt) REVERT: B 149 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6662 (mpt) REVERT: D 198 LYS cc_start: 0.7917 (pttp) cc_final: 0.7699 (mtmp) REVERT: E 188 LEU cc_start: 0.4167 (OUTLIER) cc_final: 0.3909 (tt) REVERT: E 249 GLU cc_start: 0.7760 (pm20) cc_final: 0.7289 (tt0) REVERT: E 280 TYR cc_start: 0.7829 (m-80) cc_final: 0.7517 (m-80) outliers start: 31 outliers final: 19 residues processed: 161 average time/residue: 1.2959 time to fit residues: 227.8399 Evaluate side-chains 157 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 193 ASN E 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12860 Z= 0.313 Angle : 0.672 9.019 17521 Z= 0.334 Chirality : 0.050 0.382 1855 Planarity : 0.005 0.057 2234 Dihedral : 14.212 178.142 1887 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.18 % Favored : 91.55 % Rotamer: Outliers : 1.82 % Allowed : 16.79 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.24 (0.21), residues: 1515 helix: 0.38 (0.27), residues: 373 sheet: -0.52 (0.29), residues: 325 loop : -1.54 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 466 HIS 0.005 0.001 HIS E 351 PHE 0.011 0.002 PHE A 917 TYR 0.020 0.002 TYR A 432 ARG 0.013 0.001 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.264 Fit side-chains REVERT: A 175 ARG cc_start: 0.7701 (ttp-110) cc_final: 0.7404 (mtm110) REVERT: A 531 TYR cc_start: 0.7806 (m-80) cc_final: 0.7247 (m-80) REVERT: A 533 GLN cc_start: 0.6644 (mm-40) cc_final: 0.5902 (tt0) REVERT: A 650 LEU cc_start: 0.8839 (tp) cc_final: 0.8599 (tp) REVERT: A 653 ARG cc_start: 0.7006 (ttp-110) cc_final: 0.6783 (mtm-85) REVERT: A 772 TRP cc_start: 0.8330 (t-100) cc_final: 0.7993 (t-100) REVERT: A 868 MET cc_start: 0.9055 (mtt) cc_final: 0.8802 (mtt) REVERT: A 934 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7087 (mt0) REVERT: B 51 TYR cc_start: 0.7023 (m-80) cc_final: 0.6672 (m-80) REVERT: B 75 ILE cc_start: 0.8670 (mt) cc_final: 0.8349 (mm) REVERT: B 109 ASP cc_start: 0.7174 (t70) cc_final: 0.6728 (t0) REVERT: D 198 LYS cc_start: 0.7999 (pttp) cc_final: 0.7762 (mtmp) REVERT: E 188 LEU cc_start: 0.4253 (OUTLIER) cc_final: 0.3995 (tt) REVERT: E 280 TYR cc_start: 0.7834 (m-80) cc_final: 0.7522 (m-80) outliers start: 24 outliers final: 17 residues processed: 154 average time/residue: 1.2956 time to fit residues: 217.5161 Evaluate side-chains 151 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 92 optimal weight: 6.9990 chunk 73 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN E 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12860 Z= 0.181 Angle : 0.614 10.911 17521 Z= 0.304 Chirality : 0.047 0.402 1855 Planarity : 0.004 0.058 2234 Dihedral : 13.771 176.823 1887 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.19 % Favored : 92.61 % Rotamer: Outliers : 1.74 % Allowed : 16.94 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.08 (0.22), residues: 1515 helix: 0.70 (0.27), residues: 371 sheet: -0.54 (0.29), residues: 323 loop : -1.48 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 213 HIS 0.005 0.001 HIS A 269 PHE 0.007 0.001 PHE A 405 TYR 0.022 0.001 TYR D 307 ARG 0.014 0.000 ARG A 649 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.386 Fit side-chains REVERT: A 175 ARG cc_start: 0.7725 (ttp-110) cc_final: 0.7469 (mtm110) REVERT: A 230 GLN cc_start: 0.8284 (tp40) cc_final: 0.7946 (tm-30) REVERT: A 533 GLN cc_start: 0.6544 (mm-40) cc_final: 0.5828 (tt0) REVERT: A 565 THR cc_start: 0.7209 (t) cc_final: 0.6980 (t) REVERT: A 650 LEU cc_start: 0.8812 (tp) cc_final: 0.8566 (tp) REVERT: A 653 ARG cc_start: 0.6901 (ttp-110) cc_final: 0.6664 (mtm-85) REVERT: A 703 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 772 TRP cc_start: 0.8311 (t-100) cc_final: 0.8013 (t-100) REVERT: A 868 MET cc_start: 0.9019 (mtt) cc_final: 0.8705 (mtt) REVERT: A 934 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6607 (mp-120) REVERT: B 51 TYR cc_start: 0.6983 (m-80) cc_final: 0.6703 (m-80) REVERT: B 75 ILE cc_start: 0.8622 (mt) cc_final: 0.8327 (mm) REVERT: B 89 MET cc_start: 0.8684 (mmm) cc_final: 0.8351 (tpt) REVERT: D 198 LYS cc_start: 0.7901 (pttp) cc_final: 0.7680 (mtmp) REVERT: E 188 LEU cc_start: 0.4233 (OUTLIER) cc_final: 0.4030 (tt) REVERT: E 249 GLU cc_start: 0.7740 (pm20) cc_final: 0.7356 (tt0) REVERT: E 280 TYR cc_start: 0.7861 (m-80) cc_final: 0.7550 (m-80) outliers start: 23 outliers final: 17 residues processed: 155 average time/residue: 1.2521 time to fit residues: 211.8110 Evaluate side-chains 153 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.0020 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.0030 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120631 restraints weight = 13879.896| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.39 r_work: 0.3200 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12860 Z= 0.330 Angle : 0.670 9.965 17521 Z= 0.334 Chirality : 0.050 0.397 1855 Planarity : 0.005 0.061 2234 Dihedral : 13.657 177.432 1887 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.38 % Favored : 91.42 % Rotamer: Outliers : 1.82 % Allowed : 17.10 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.22), residues: 1515 helix: 0.47 (0.27), residues: 373 sheet: -0.52 (0.29), residues: 327 loop : -1.50 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 466 HIS 0.005 0.001 HIS A 592 PHE 0.012 0.002 PHE A 405 TYR 0.022 0.002 TYR A 432 ARG 0.016 0.001 ARG A 649 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4601.80 seconds wall clock time: 83 minutes 34.99 seconds (5014.99 seconds total)