Starting phenix.real_space_refine on Thu Feb 15 17:58:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p1h_20235/02_2024/6p1h_20235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p1h_20235/02_2024/6p1h_20235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p1h_20235/02_2024/6p1h_20235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p1h_20235/02_2024/6p1h_20235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p1h_20235/02_2024/6p1h_20235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p1h_20235/02_2024/6p1h_20235_updated.pdb" } resolution = 3.2 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= 0.011 sd= 1.053 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 Fe 4 7.16 5 P 30 5.49 5 S 67 5.16 5 C 8171 2.51 5 N 2180 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 99": "NH1" <-> "NH2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ASP 506": "OD1" <-> "OD2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 641": "OD1" <-> "OD2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A ASP 780": "OD1" <-> "OD2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 831": "OD1" <-> "OD2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A ARG 881": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 923": "NH1" <-> "NH2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A GLU 1033": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ASP 265": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 372": "OD1" <-> "OD2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ASP 102": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13006 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7691 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 920} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3755 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 27, 'TRANS': 441} Chain breaks: 2 Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 921 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 233 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 40 Unusual residues: {' CA': 4, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7452 SG CYS A1069 62.579 62.764 63.623 1.00 91.25 S ATOM 7489 SG CYS A1074 64.626 65.090 58.264 1.00 84.90 S ATOM 7355 SG CYS A1056 58.493 66.521 60.923 1.00 96.71 S ATOM 7381 SG CYS A1059 60.216 60.875 58.005 1.00 95.96 S Time building chain proxies: 7.40, per 1000 atoms: 0.57 Number of scatterers: 13006 At special positions: 0 Unit cell: (143.623, 129.945, 100.023, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 5 19.99 S 67 16.00 P 30 15.00 O 2549 8.00 N 2180 7.00 C 8171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1101 " pdb="FE1 SF4 A1101 " - pdb=" SG CYS A1069 " pdb="FE2 SF4 A1101 " - pdb=" SG CYS A1074 " pdb="FE4 SF4 A1101 " - pdb=" SG CYS A1059 " pdb="FE3 SF4 A1101 " - pdb=" SG CYS A1056 " Number of angles added : 12 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 15 sheets defined 30.3% alpha, 12.0% beta 12 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 173 through 186 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.644A pdb=" N ARG A 233 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 379 through 393 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 507 through 531 Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 533 through 543 Processing helix chain 'A' and resid 548 through 551 No H-bonds generated for 'chain 'A' and resid 548 through 551' Processing helix chain 'A' and resid 557 through 571 Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.611A pdb=" N ARG A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP A 680 " --> pdb=" O ARG A 676 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 697 No H-bonds generated for 'chain 'A' and resid 694 through 697' Processing helix chain 'A' and resid 705 through 712 removed outlier: 3.516A pdb=" N THR A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 728 No H-bonds generated for 'chain 'A' and resid 725 through 728' Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.775A pdb=" N THR A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 792 removed outlier: 3.591A pdb=" N GLU A 784 " --> pdb=" O ASP A 780 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 792 " --> pdb=" O TYR A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 858 Processing helix chain 'A' and resid 863 through 878 Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 902 through 914 Processing helix chain 'A' and resid 942 through 948 removed outlier: 3.531A pdb=" N GLU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 960 Processing helix chain 'A' and resid 962 through 974 Proline residue: A 972 - end of helix Processing helix chain 'A' and resid 976 through 983 removed outlier: 4.023A pdb=" N PHE A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1036 Processing helix chain 'A' and resid 1042 through 1060 removed outlier: 4.405A pdb=" N GLU A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN A1057 " --> pdb=" O TRP A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1094 removed outlier: 3.516A pdb=" N GLU A1089 " --> pdb=" O LYS A1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 55 through 72 removed outlier: 4.526A pdb=" N GLU B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.809A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 322 through 328 removed outlier: 4.283A pdb=" N SER B 326 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 394 through 404 Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'C' and resid 22 through 28 removed outlier: 3.916A pdb=" N ILE C 26 " --> pdb=" O PHE C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 45 removed outlier: 4.909A pdb=" N LYS C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.986A pdb=" N SER A 268 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 137 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 151 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 121 through 124 Processing sheet with id= C, first strand: chain 'A' and resid 159 through 163 removed outlier: 3.786A pdb=" N SER A 193 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 317 through 319 removed outlier: 6.226A pdb=" N VAL A 397 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU A 460 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N GLY A 400 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 462 " --> pdb=" O GLY A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 358 through 361 removed outlier: 6.894A pdb=" N GLU A 323 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A 342 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP A 321 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 436 through 441 Processing sheet with id= G, first strand: chain 'A' and resid 598 through 600 Processing sheet with id= H, first strand: chain 'A' and resid 644 through 646 Processing sheet with id= I, first strand: chain 'A' and resid 889 through 892 Processing sheet with id= J, first strand: chain 'A' and resid 604 through 609 removed outlier: 3.707A pdb=" N LYS A 803 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP A 608 " --> pdb=" O PHE A 801 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE A 801 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 816 through 821 removed outlier: 3.804A pdb=" N LYS A 829 " --> pdb=" O PHE A 820 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 184 through 186 removed outlier: 8.460A pdb=" N PHE B 185 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 156 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY B 153 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 155 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 146 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 102 " --> pdb=" O GLY B 177 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 106 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 173 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.274A pdb=" N ARG B 256 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 343 through 347 removed outlier: 3.525A pdb=" N TYR B 347 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 435 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 445 through 451 removed outlier: 3.670A pdb=" N GLY B 445 " --> pdb=" O SER B 460 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 5412 1.40 - 1.62: 7765 1.62 - 1.84: 99 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 13288 Sorted by residual: bond pdb=" C3' DCP A1102 " pdb=" C4' DCP A1102 " ideal model delta sigma weight residual 1.527 1.335 0.192 1.10e-02 8.26e+03 3.05e+02 bond pdb=" C4' DCP A1102 " pdb=" O4' DCP A1102 " ideal model delta sigma weight residual 1.444 1.603 -0.159 1.00e-02 1.00e+04 2.52e+02 bond pdb=" C4 DCP A1102 " pdb=" N4 DCP A1102 " ideal model delta sigma weight residual 1.334 1.466 -0.132 1.20e-02 6.94e+03 1.21e+02 bond pdb=" C1' DCP A1102 " pdb=" O4' DCP A1102 " ideal model delta sigma weight residual 1.418 1.291 0.127 1.20e-02 6.94e+03 1.12e+02 bond pdb=" C5 DCP A1102 " pdb=" C6 DCP A1102 " ideal model delta sigma weight residual 1.345 1.495 -0.150 1.80e-02 3.09e+03 6.99e+01 ... (remaining 13283 not shown) Histogram of bond angle deviations from ideal: 73.73 - 85.77: 12 85.77 - 97.82: 0 97.82 - 109.87: 2329 109.87 - 121.92: 13199 121.92 - 133.96: 2583 Bond angle restraints: 18123 Sorted by residual: angle pdb=" PB DCP A1102 " pdb=" O3B DCP A1102 " pdb=" PG DCP A1102 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PA DCP A1102 " pdb=" O3A DCP A1102 " pdb=" PB DCP A1102 " ideal model delta sigma weight residual 136.83 119.63 17.20 1.00e+00 1.00e+00 2.96e+02 angle pdb=" C2' DCP A1102 " pdb=" C1' DCP A1102 " pdb=" N1 DCP A1102 " ideal model delta sigma weight residual 113.92 106.37 7.55 1.28e+00 6.12e-01 3.49e+01 angle pdb=" O2G DCP A1102 " pdb=" PG DCP A1102 " pdb=" O3B DCP A1102 " ideal model delta sigma weight residual 104.48 110.31 -5.83 1.14e+00 7.76e-01 2.64e+01 angle pdb=" O3A DCP A1102 " pdb=" PB DCP A1102 " pdb=" O3B DCP A1102 " ideal model delta sigma weight residual 101.57 109.28 -7.71 1.54e+00 4.24e-01 2.52e+01 ... (remaining 18118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6972 17.94 - 35.89: 774 35.89 - 53.83: 182 53.83 - 71.77: 40 71.77 - 89.71: 11 Dihedral angle restraints: 7979 sinusoidal: 3447 harmonic: 4532 Sorted by residual: dihedral pdb=" CA VAL B 87 " pdb=" C VAL B 87 " pdb=" N LEU B 88 " pdb=" CA LEU B 88 " ideal model delta harmonic sigma weight residual 180.00 -122.71 -57.29 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA PRO B 22 " pdb=" C PRO B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 dihedral pdb=" CA GLN B 85 " pdb=" C GLN B 85 " pdb=" N LEU B 86 " pdb=" CA LEU B 86 " ideal model delta harmonic sigma weight residual -180.00 -139.58 -40.42 0 5.00e+00 4.00e-02 6.53e+01 ... (remaining 7976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1497 0.054 - 0.108: 457 0.108 - 0.161: 68 0.161 - 0.215: 5 0.215 - 0.269: 2 Chirality restraints: 2029 Sorted by residual: chirality pdb=" C3' DCP A1102 " pdb=" C2' DCP A1102 " pdb=" C4' DCP A1102 " pdb=" O3' DCP A1102 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE C 109 " pdb=" CA ILE C 109 " pdb=" CG1 ILE C 109 " pdb=" CG2 ILE C 109 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE C 74 " pdb=" CA ILE C 74 " pdb=" CG1 ILE C 74 " pdb=" CG2 ILE C 74 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2026 not shown) Planarity restraints: 2223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 405 " -0.015 2.00e-02 2.50e+03 1.28e-02 4.08e+00 pdb=" CG TRP B 405 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 405 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 405 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 405 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 405 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 405 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 405 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 405 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 405 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 663 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 664 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 806 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 807 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " 0.026 5.00e-02 4.00e+02 ... (remaining 2220 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 158 2.53 - 3.12: 10728 3.12 - 3.72: 19644 3.72 - 4.31: 29404 4.31 - 4.90: 48302 Nonbonded interactions: 108236 Sorted by model distance: nonbonded pdb=" OD2 ASP A 321 " pdb="CA CA A1106 " model vdw 1.939 2.510 nonbonded pdb=" OE1 GLN A 832 " pdb=" OG SER A 837 " model vdw 2.023 2.440 nonbonded pdb=" OD2 ASP B 297 " pdb=" OH TYR B 347 " model vdw 2.167 2.440 nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASP B 307 " model vdw 2.176 2.440 nonbonded pdb=" O ASP A 337 " pdb=" OH TYR A 410 " model vdw 2.181 2.440 ... (remaining 108231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.350 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: 0.020 Extract box with map and model: 7.560 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 42.770 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.009 0.192 13288 Z= 0.581 Angle : 0.888 19.607 18123 Z= 0.533 Chirality : 0.051 0.269 2029 Planarity : 0.005 0.046 2223 Dihedral : 15.972 89.712 5057 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.17 % Favored : 90.18 % Rotamer: Outliers : 0.07 % Allowed : 8.69 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % 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: -3.47 (0.18), residues: 1527 helix: -1.69 (0.19), residues: 504 sheet: -2.96 (0.29), residues: 217 loop : -2.53 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 405 HIS 0.005 0.001 HIS C 27 PHE 0.021 0.002 PHE A 806 TYR 0.020 0.002 TYR A 805 ARG 0.006 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8392 (mmmt) REVERT: A 1089 GLU cc_start: 0.8294 (tp30) cc_final: 0.7963 (tp30) REVERT: A 1092 GLU cc_start: 0.8551 (tp30) cc_final: 0.8289 (tp30) REVERT: B 5 LEU cc_start: 0.7141 (mm) cc_final: 0.6228 (mm) REVERT: B 211 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7695 (tpp80) REVERT: C 8 PHE cc_start: 0.7380 (t80) cc_final: 0.7110 (t80) REVERT: C 41 PHE cc_start: 0.8960 (t80) cc_final: 0.8717 (t80) REVERT: C 62 ASP cc_start: 0.8614 (p0) cc_final: 0.8397 (p0) REVERT: C 89 ASN cc_start: 0.6604 (t0) cc_final: 0.5119 (t0) REVERT: C 91 MET cc_start: 0.7870 (mpp) cc_final: 0.7001 (tmm) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2756 time to fit residues: 71.2724 Evaluate side-chains 148 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 171 ASN A 175 GLN A 181 HIS A 283 ASN A 284 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 434 GLN A 485 HIS A 750 ASN A 880 ASN A 949 ASN A 951 GLN A 980 ASN A1073 ASN A1088 GLN A1093 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 124 ASN B 272 ASN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 332 ASN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13288 Z= 0.194 Angle : 0.643 10.747 18123 Z= 0.331 Chirality : 0.045 0.247 2029 Planarity : 0.005 0.044 2223 Dihedral : 14.147 89.869 1995 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.27 % Favored : 92.40 % Rotamer: Outliers : 1.29 % Allowed : 12.14 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % 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: -2.31 (0.20), residues: 1527 helix: -0.34 (0.23), residues: 508 sheet: -2.68 (0.30), residues: 230 loop : -1.97 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 417 HIS 0.005 0.001 HIS C 27 PHE 0.015 0.001 PHE C 88 TYR 0.016 0.001 TYR C 44 ARG 0.004 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8612 (mmmm) cc_final: 0.8319 (mmmt) REVERT: A 698 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8826 (tt) REVERT: A 912 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7692 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8208 (tp30) cc_final: 0.7929 (tp30) REVERT: A 1092 GLU cc_start: 0.8523 (tp30) cc_final: 0.8248 (tp30) REVERT: B 53 TYR cc_start: 0.8448 (m-80) cc_final: 0.8247 (m-10) REVERT: C 41 PHE cc_start: 0.8913 (t80) cc_final: 0.8587 (t80) REVERT: C 52 TYR cc_start: 0.5241 (p90) cc_final: 0.4258 (p90) REVERT: C 62 ASP cc_start: 0.8672 (p0) cc_final: 0.8218 (p0) REVERT: C 89 ASN cc_start: 0.6843 (t0) cc_final: 0.6579 (p0) outliers start: 18 outliers final: 12 residues processed: 183 average time/residue: 0.2368 time to fit residues: 65.5178 Evaluate side-chains 161 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 59 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 705 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13288 Z= 0.342 Angle : 0.676 11.672 18123 Z= 0.345 Chirality : 0.046 0.228 2029 Planarity : 0.004 0.042 2223 Dihedral : 14.101 89.778 1995 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.99 % Favored : 91.68 % Rotamer: Outliers : 2.59 % Allowed : 13.51 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % 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: -2.02 (0.21), residues: 1527 helix: -0.04 (0.23), residues: 505 sheet: -2.51 (0.29), residues: 241 loop : -1.82 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 PHE 0.013 0.001 PHE B 345 TYR 0.025 0.002 TYR C 43 ARG 0.004 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8399 (mmmt) REVERT: A 698 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8814 (tt) REVERT: A 912 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7717 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8263 (tp30) cc_final: 0.7887 (tp30) REVERT: A 1092 GLU cc_start: 0.8509 (tp30) cc_final: 0.8266 (tp30) REVERT: C 24 ASP cc_start: 0.8870 (m-30) cc_final: 0.8526 (p0) REVERT: C 62 ASP cc_start: 0.8851 (p0) cc_final: 0.8560 (p0) REVERT: C 89 ASN cc_start: 0.7092 (t0) cc_final: 0.5987 (t0) REVERT: C 90 PRO cc_start: 0.7656 (Cg_exo) cc_final: 0.7252 (Cg_endo) REVERT: C 91 MET cc_start: 0.8578 (pmm) cc_final: 0.7921 (pmm) outliers start: 36 outliers final: 26 residues processed: 169 average time/residue: 0.2273 time to fit residues: 59.0292 Evaluate side-chains 170 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13288 Z= 0.225 Angle : 0.624 10.486 18123 Z= 0.318 Chirality : 0.044 0.222 2029 Planarity : 0.004 0.040 2223 Dihedral : 13.886 89.901 1995 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.27 % Favored : 92.47 % Rotamer: Outliers : 2.95 % Allowed : 15.66 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.69 (0.21), residues: 1527 helix: 0.16 (0.24), residues: 504 sheet: -2.19 (0.29), residues: 253 loop : -1.60 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 417 HIS 0.007 0.001 HIS C 28 PHE 0.022 0.001 PHE C 84 TYR 0.015 0.001 TYR C 43 ARG 0.006 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8291 (mmmt) REVERT: A 912 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7769 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8247 (tp30) cc_final: 0.8033 (tp30) REVERT: A 1092 GLU cc_start: 0.8498 (tp30) cc_final: 0.8260 (tp30) REVERT: B 35 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5752 (p0) REVERT: B 431 LYS cc_start: 0.8980 (pttp) cc_final: 0.8727 (pttm) REVERT: B 476 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 62 ASP cc_start: 0.8890 (p0) cc_final: 0.8566 (p0) REVERT: C 89 ASN cc_start: 0.7079 (t0) cc_final: 0.6066 (t0) REVERT: C 91 MET cc_start: 0.8556 (pmm) cc_final: 0.7977 (pmm) outliers start: 41 outliers final: 28 residues processed: 185 average time/residue: 0.2225 time to fit residues: 64.3545 Evaluate side-chains 176 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 109 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 754 HIS ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13288 Z= 0.445 Angle : 0.702 9.598 18123 Z= 0.358 Chirality : 0.047 0.225 2029 Planarity : 0.005 0.043 2223 Dihedral : 14.061 89.822 1995 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.64 % Favored : 91.16 % Rotamer: Outliers : 3.59 % Allowed : 15.73 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: 1527 helix: 0.04 (0.24), residues: 504 sheet: -2.09 (0.30), residues: 244 loop : -1.62 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 417 HIS 0.006 0.001 HIS C 28 PHE 0.025 0.002 PHE C 84 TYR 0.016 0.002 TYR A 220 ARG 0.006 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 144 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8971 (tt0) REVERT: A 491 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8453 (mmmt) REVERT: A 698 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8842 (tt) REVERT: A 1089 GLU cc_start: 0.8256 (tp30) cc_final: 0.7891 (tp30) REVERT: A 1092 GLU cc_start: 0.8492 (tp30) cc_final: 0.8275 (tp30) REVERT: B 35 ASN cc_start: 0.6103 (OUTLIER) cc_final: 0.5842 (p0) REVERT: B 476 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7704 (mm-30) REVERT: C 62 ASP cc_start: 0.8911 (p0) cc_final: 0.8501 (p0) REVERT: C 89 ASN cc_start: 0.7056 (t0) cc_final: 0.6076 (t0) REVERT: C 91 MET cc_start: 0.8542 (pmm) cc_final: 0.8024 (pmm) outliers start: 50 outliers final: 36 residues processed: 182 average time/residue: 0.2082 time to fit residues: 58.9745 Evaluate side-chains 182 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13288 Z= 0.188 Angle : 0.614 9.308 18123 Z= 0.313 Chirality : 0.044 0.227 2029 Planarity : 0.004 0.041 2223 Dihedral : 13.779 89.062 1995 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.14 % Favored : 92.60 % Rotamer: Outliers : 3.16 % Allowed : 16.45 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: 1527 helix: 0.28 (0.24), residues: 504 sheet: -1.95 (0.30), residues: 248 loop : -1.52 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 PHE 0.016 0.001 PHE C 41 TYR 0.020 0.001 TYR C 43 ARG 0.007 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8578 (mmmm) cc_final: 0.8267 (mmmt) REVERT: A 698 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8789 (tt) REVERT: A 912 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7739 (mtm110) REVERT: A 1089 GLU cc_start: 0.8248 (tp30) cc_final: 0.7947 (tp30) REVERT: A 1092 GLU cc_start: 0.8510 (tp30) cc_final: 0.8275 (tp30) REVERT: B 35 ASN cc_start: 0.5976 (OUTLIER) cc_final: 0.5724 (p0) REVERT: B 431 LYS cc_start: 0.8991 (pttp) cc_final: 0.8742 (pttm) REVERT: B 469 MET cc_start: 0.8197 (mtm) cc_final: 0.7908 (ttm) REVERT: B 470 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8000 (pt) REVERT: B 476 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7729 (mm-30) REVERT: C 62 ASP cc_start: 0.8959 (p0) cc_final: 0.8584 (p0) REVERT: C 63 GLN cc_start: 0.8104 (mp10) cc_final: 0.7845 (pm20) REVERT: C 89 ASN cc_start: 0.7084 (t0) cc_final: 0.6063 (t0) REVERT: C 91 MET cc_start: 0.8477 (pmm) cc_final: 0.8029 (pmm) outliers start: 44 outliers final: 31 residues processed: 185 average time/residue: 0.2587 time to fit residues: 73.5966 Evaluate side-chains 178 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 109 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.3980 chunk 16 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS B 337 ASN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13288 Z= 0.180 Angle : 0.605 9.111 18123 Z= 0.307 Chirality : 0.043 0.250 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.497 89.951 1995 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 2.80 % Allowed : 17.82 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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 (0.22), residues: 1527 helix: 0.47 (0.24), residues: 511 sheet: -1.67 (0.31), residues: 256 loop : -1.39 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1053 HIS 0.009 0.001 HIS A 495 PHE 0.047 0.001 PHE C 8 TYR 0.011 0.001 TYR A 805 ARG 0.007 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8210 (mmmt) REVERT: A 912 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7683 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8252 (tp30) cc_final: 0.7919 (tp30) REVERT: A 1092 GLU cc_start: 0.8501 (tp30) cc_final: 0.8289 (tp30) REVERT: B 476 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7681 (mm-30) REVERT: C 62 ASP cc_start: 0.8997 (p0) cc_final: 0.8605 (p0) REVERT: C 63 GLN cc_start: 0.8193 (mp10) cc_final: 0.7936 (pm20) REVERT: C 89 ASN cc_start: 0.7133 (t0) cc_final: 0.6895 (p0) REVERT: C 91 MET cc_start: 0.8395 (pmm) cc_final: 0.8113 (pmm) outliers start: 39 outliers final: 31 residues processed: 186 average time/residue: 0.2070 time to fit residues: 59.6504 Evaluate side-chains 175 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 109 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 620 HIS ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 13288 Z= 0.432 Angle : 0.693 9.271 18123 Z= 0.353 Chirality : 0.047 0.293 2029 Planarity : 0.004 0.041 2223 Dihedral : 13.872 89.680 1995 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.58 % Favored : 91.36 % Rotamer: Outliers : 3.23 % Allowed : 17.67 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.43 (0.21), residues: 1527 helix: 0.25 (0.24), residues: 507 sheet: -1.69 (0.32), residues: 249 loop : -1.49 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 417 HIS 0.006 0.001 HIS A 495 PHE 0.026 0.002 PHE C 84 TYR 0.024 0.002 TYR C 43 ARG 0.006 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 912 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7628 (mtm-85) REVERT: A 947 GLU cc_start: 0.8014 (tt0) cc_final: 0.7745 (tm-30) REVERT: A 1089 GLU cc_start: 0.8280 (tp30) cc_final: 0.7932 (tp30) REVERT: A 1092 GLU cc_start: 0.8512 (tp30) cc_final: 0.8307 (tp30) REVERT: B 476 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7710 (mm-30) REVERT: C 62 ASP cc_start: 0.8975 (p0) cc_final: 0.8539 (p0) REVERT: C 63 GLN cc_start: 0.8302 (mp10) cc_final: 0.7934 (pm20) REVERT: C 89 ASN cc_start: 0.7200 (t0) cc_final: 0.6136 (t0) REVERT: C 91 MET cc_start: 0.8326 (pmm) cc_final: 0.7856 (pmm) outliers start: 45 outliers final: 37 residues processed: 177 average time/residue: 0.2250 time to fit residues: 62.0676 Evaluate side-chains 180 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN A 495 HIS ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN C 27 HIS ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13288 Z= 0.227 Angle : 0.631 9.888 18123 Z= 0.319 Chirality : 0.044 0.306 2029 Planarity : 0.004 0.041 2223 Dihedral : 13.648 89.191 1995 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.67 % Rotamer: Outliers : 2.59 % Allowed : 18.68 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.22), residues: 1527 helix: 0.39 (0.24), residues: 505 sheet: -1.67 (0.31), residues: 256 loop : -1.38 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 417 HIS 0.009 0.001 HIS A 495 PHE 0.040 0.002 PHE C 8 TYR 0.017 0.001 TYR C 43 ARG 0.007 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8253 (mmmt) REVERT: A 850 MET cc_start: 0.8781 (mmm) cc_final: 0.8499 (mmt) REVERT: A 912 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7673 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8264 (tp30) cc_final: 0.7968 (tp30) REVERT: B 476 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7667 (mm-30) REVERT: C 48 THR cc_start: 0.5087 (p) cc_final: 0.4878 (m) REVERT: C 62 ASP cc_start: 0.9004 (p0) cc_final: 0.8583 (p0) REVERT: C 63 GLN cc_start: 0.8270 (mp10) cc_final: 0.7932 (pm20) REVERT: C 89 ASN cc_start: 0.7285 (t0) cc_final: 0.6352 (t0) REVERT: C 91 MET cc_start: 0.8265 (pmm) cc_final: 0.7805 (pmm) outliers start: 36 outliers final: 33 residues processed: 172 average time/residue: 0.2122 time to fit residues: 56.8271 Evaluate side-chains 174 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.0270 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13288 Z= 0.255 Angle : 0.638 10.011 18123 Z= 0.322 Chirality : 0.045 0.342 2029 Planarity : 0.004 0.041 2223 Dihedral : 13.601 89.436 1995 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.86 % Favored : 92.08 % Rotamer: Outliers : 2.59 % Allowed : 18.53 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.25 (0.22), residues: 1527 helix: 0.43 (0.24), residues: 505 sheet: -1.65 (0.31), residues: 256 loop : -1.36 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 417 HIS 0.009 0.001 HIS A 495 PHE 0.023 0.001 PHE C 84 TYR 0.015 0.001 TYR C 43 ARG 0.007 0.000 ARG A 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8298 (mmmt) REVERT: A 850 MET cc_start: 0.8770 (mmm) cc_final: 0.8483 (mmt) REVERT: A 912 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7686 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8270 (tp30) cc_final: 0.7920 (tp30) REVERT: A 1092 GLU cc_start: 0.8380 (tp30) cc_final: 0.8154 (tm-30) REVERT: B 476 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 29 LEU cc_start: 0.9220 (mp) cc_final: 0.8731 (tp) REVERT: C 62 ASP cc_start: 0.8995 (p0) cc_final: 0.8534 (p0) REVERT: C 63 GLN cc_start: 0.8350 (mp10) cc_final: 0.8032 (pm20) REVERT: C 88 PHE cc_start: 0.8652 (m-80) cc_final: 0.8418 (m-80) REVERT: C 89 ASN cc_start: 0.7464 (t0) cc_final: 0.6679 (t0) REVERT: C 91 MET cc_start: 0.8122 (pmm) cc_final: 0.6776 (ppp) outliers start: 36 outliers final: 33 residues processed: 171 average time/residue: 0.2095 time to fit residues: 55.8919 Evaluate side-chains 175 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077873 restraints weight = 23431.243| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.72 r_work: 0.2983 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 13288 Z= 0.170 Angle : 0.607 10.589 18123 Z= 0.306 Chirality : 0.043 0.316 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.379 88.882 1995 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 2.30 % Allowed : 19.04 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -1.10 (0.22), residues: 1527 helix: 0.59 (0.24), residues: 505 sheet: -1.65 (0.31), residues: 264 loop : -1.26 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 103 HIS 0.010 0.001 HIS A 495 PHE 0.046 0.001 PHE C 8 TYR 0.016 0.001 TYR C 43 ARG 0.007 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.03 seconds wall clock time: 48 minutes 51.45 seconds (2931.45 seconds total)