Starting phenix.real_space_refine on Tue Mar 19 20:30:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/03_2024/7yi4_33851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/03_2024/7yi4_33851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/03_2024/7yi4_33851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/03_2024/7yi4_33851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/03_2024/7yi4_33851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi4_33851/03_2024/7yi4_33851_updated.pdb" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 5 6.06 5 P 302 5.49 5 S 87 5.16 5 C 15143 2.51 5 N 4495 2.21 5 O 5319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 715": "OE1" <-> "OE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 553": "OD1" <-> "OD2" Residue "I GLU 41": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "K ASP 81": "OD1" <-> "OD2" Residue "K GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25351 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2326 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2588 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 5 Chain: "F" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "H" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3076 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "P" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3115 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11022 SG CYS D 417 127.085 60.757 70.222 1.00548.42 S ATOM 11049 SG CYS D 420 128.395 57.216 70.769 1.00541.45 S ATOM 11305 SG CYS D 451 128.651 59.913 73.503 1.00488.09 S ATOM 9961 SG CYS D 263 92.512 95.032 76.495 1.00502.95 S ATOM 9978 SG CYS D 266 95.322 92.480 76.314 1.00506.17 S ATOM 10131 SG CYS D 286 96.001 95.688 78.071 1.00483.68 S ATOM 10266 SG CYS D 303 84.724 101.733 74.705 1.00517.62 S ATOM 10289 SG CYS D 306 80.870 104.261 73.937 1.00523.12 S ATOM 11210 SG CYS D 440 121.918 69.864 66.373 1.00572.63 S ATOM 11236 SG CYS D 443 124.633 69.527 63.545 1.00575.36 S ATOM 11425 SG CYS D 466 125.622 71.045 66.672 1.00567.07 S Time building chain proxies: 12.09, per 1000 atoms: 0.48 Number of scatterers: 25351 At special positions: 0 Unit cell: (177.53, 149.385, 145.055, 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 5 29.99 S 87 16.00 P 302 15.00 O 5319 8.00 N 4495 7.00 C 15143 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: 12.75 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 451 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 420 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 263 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 303 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 306 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 440 " Number of angles added : 9 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 9 sheets defined 51.7% alpha, 5.2% beta 147 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 11.26 Creating SS restraints... Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 716 through 723 Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 786 through 789 No H-bonds generated for 'chain 'A' and resid 786 through 789' Processing helix chain 'A' and resid 802 through 837 Processing helix chain 'A' and resid 862 through 870 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 891 through 921 Processing helix chain 'A' and resid 924 through 927 No H-bonds generated for 'chain 'A' and resid 924 through 927' Processing helix chain 'A' and resid 930 through 933 No H-bonds generated for 'chain 'A' and resid 930 through 933' Processing helix chain 'A' and resid 935 through 942 Processing helix chain 'A' and resid 945 through 960 Processing helix chain 'A' and resid 984 through 998 Processing helix chain 'A' and resid 1004 through 1022 Processing helix chain 'A' and resid 1142 through 1163 Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1190 through 1193 No H-bonds generated for 'chain 'A' and resid 1190 through 1193' Processing helix chain 'A' and resid 1203 through 1216 Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1237 through 1239 No H-bonds generated for 'chain 'A' and resid 1237 through 1239' Processing helix chain 'A' and resid 1242 through 1258 Processing helix chain 'A' and resid 1260 through 1275 Processing helix chain 'A' and resid 1280 through 1293 removed outlier: 3.636A pdb=" N GLN A1283 " --> pdb=" O ALA A1280 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 4.077A pdb=" N GLY B 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.624A pdb=" N ASN B 54 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.590A pdb=" N GLN B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 116 through 136 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 244 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 288 through 301 removed outlier: 4.321A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 344 through 347 Processing helix chain 'B' and resid 366 through 382 removed outlier: 4.574A pdb=" N ASN B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 72 No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 102 through 123 Processing helix chain 'C' and resid 226 through 240 Processing helix chain 'C' and resid 254 through 266 Processing helix chain 'C' and resid 272 through 296 removed outlier: 5.251A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.811A pdb=" N SER C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 344 removed outlier: 3.985A pdb=" N SER C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 368 removed outlier: 3.934A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 400 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 169 through 174 removed outlier: 3.849A pdb=" N THR D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU D 173 " --> pdb=" O PHE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 186 removed outlier: 4.478A pdb=" N GLY D 186 " --> pdb=" O SER D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 186' Processing helix chain 'D' and resid 304 through 311 Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 337 through 345 removed outlier: 4.296A pdb=" N ASP D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 406 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 544 through 563 removed outlier: 3.580A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 562 Processing helix chain 'H' and resid 25 through 28 Processing helix chain 'H' and resid 31 through 40 Processing helix chain 'H' and resid 50 through 75 removed outlier: 3.892A pdb=" N ASP H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'I' and resid 17 through 21 Processing helix chain 'I' and resid 27 through 37 Processing helix chain 'I' and resid 47 through 72 Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 113 through 115 No H-bonds generated for 'chain 'I' and resid 113 through 115' Processing helix chain 'J' and resid 35 through 45 Processing helix chain 'J' and resid 53 through 80 Processing helix chain 'J' and resid 88 through 98 Processing helix chain 'J' and resid 102 through 120 Processing helix chain 'L' and resid 26 through 28 No H-bonds generated for 'chain 'L' and resid 26 through 28' Processing helix chain 'L' and resid 31 through 40 Processing helix chain 'L' and resid 48 through 75 removed outlier: 4.144A pdb=" N TYR L 51 " --> pdb=" O GLY L 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU L 52 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG L 67 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 92 Processing helix chain 'M' and resid 17 through 21 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 47 through 72 Processing helix chain 'M' and resid 80 through 89 Processing helix chain 'M' and resid 91 through 96 Processing helix chain 'N' and resid 35 through 45 Processing helix chain 'N' and resid 53 through 80 Processing helix chain 'N' and resid 88 through 98 Processing helix chain 'N' and resid 101 through 120 Processing helix chain 'E' and resid 69 through 72 No H-bonds generated for 'chain 'E' and resid 69 through 72' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 102 through 123 Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 64 through 74 Processing helix chain 'G' and resid 86 through 114 Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.594A pdb=" N LYS K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 77 removed outlier: 3.974A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 Processing helix chain 'K' and resid 121 through 131 Processing sheet with id= A, first strand: chain 'A' and resid 975 through 978 Processing sheet with id= B, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.621A pdb=" N VAL B 141 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE B 24 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 143 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET B 305 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ASN B 144 " --> pdb=" O MET B 305 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL B 307 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 13 through 18 removed outlier: 6.522A pdb=" N PHE C 78 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 29 through 32 Processing sheet with id= E, first strand: chain 'C' and resid 244 through 246 Processing sheet with id= F, first strand: chain 'D' and resid 364 through 366 Processing sheet with id= G, first strand: chain 'D' and resid 473 through 476 Processing sheet with id= H, first strand: chain 'E' and resid 13 through 18 removed outlier: 3.854A pdb=" N CYS E 14 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E 25 " --> pdb=" O CYS E 14 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE E 78 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE E 30 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS E 76 " --> pdb=" O ILE E 30 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 29 through 32 887 hydrogen bonds defined for protein. 2451 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 14.13 Time building geometry restraints manager: 13.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6819 1.34 - 1.46: 6865 1.46 - 1.58: 12052 1.58 - 1.70: 602 1.70 - 1.82: 137 Bond restraints: 26475 Sorted by residual: bond pdb=" CG MET B 47 " pdb=" SD MET B 47 " ideal model delta sigma weight residual 1.803 1.748 0.055 2.50e-02 1.60e+03 4.91e+00 bond pdb=" CB ARG E 110 " pdb=" CG ARG E 110 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CA MET B 305 " pdb=" CB MET B 305 " ideal model delta sigma weight residual 1.535 1.564 -0.029 2.09e-02 2.29e+03 1.88e+00 bond pdb=" N ALA M 47 " pdb=" CA ALA M 47 " ideal model delta sigma weight residual 1.463 1.454 0.009 6.90e-03 2.10e+04 1.62e+00 bond pdb=" CA LEU L 49 " pdb=" CB LEU L 49 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.34e-02 5.57e+03 1.40e+00 ... (remaining 26470 not shown) Histogram of bond angle deviations from ideal: 96.47 - 103.99: 1135 103.99 - 111.50: 12779 111.50 - 119.02: 8921 119.02 - 126.54: 13066 126.54 - 134.05: 1107 Bond angle restraints: 37008 Sorted by residual: angle pdb=" CA MET A1164 " pdb=" CB MET A1164 " pdb=" CG MET A1164 " ideal model delta sigma weight residual 114.10 125.18 -11.08 2.00e+00 2.50e-01 3.07e+01 angle pdb=" CA MET B 47 " pdb=" CB MET B 47 " pdb=" CG MET B 47 " ideal model delta sigma weight residual 114.10 124.46 -10.36 2.00e+00 2.50e-01 2.69e+01 angle pdb=" CA LEU L 49 " pdb=" CB LEU L 49 " pdb=" CG LEU L 49 " ideal model delta sigma weight residual 116.30 133.57 -17.27 3.50e+00 8.16e-02 2.43e+01 angle pdb=" N MET B 47 " pdb=" CA MET B 47 " pdb=" CB MET B 47 " ideal model delta sigma weight residual 110.40 117.37 -6.97 1.63e+00 3.76e-01 1.83e+01 angle pdb=" CB ARG E 110 " pdb=" CG ARG E 110 " pdb=" CD ARG E 110 " ideal model delta sigma weight residual 111.30 121.00 -9.70 2.30e+00 1.89e-01 1.78e+01 ... (remaining 37003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 13107 31.31 - 62.62: 1975 62.62 - 93.92: 73 93.92 - 125.23: 0 125.23 - 156.54: 1 Dihedral angle restraints: 15156 sinusoidal: 8247 harmonic: 6909 Sorted by residual: dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA MET B 61 " pdb=" C MET B 61 " pdb=" N GLU B 62 " pdb=" CA GLU B 62 " ideal model delta harmonic sigma weight residual 180.00 158.77 21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA MET A1194 " pdb=" C MET A1194 " pdb=" N GLY A1195 " pdb=" CA GLY A1195 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 15153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2941 0.035 - 0.069: 879 0.069 - 0.104: 188 0.104 - 0.139: 59 0.139 - 0.173: 9 Chirality restraints: 4076 Sorted by residual: chirality pdb=" CA MET B 47 " pdb=" N MET B 47 " pdb=" C MET B 47 " pdb=" CB MET B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA GLU C 255 " pdb=" N GLU C 255 " pdb=" C GLU C 255 " pdb=" CB GLU C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA GLU A 918 " pdb=" N GLU A 918 " pdb=" C GLU A 918 " pdb=" CB GLU A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 4073 not shown) Planarity restraints: 3647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1164 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C MET A1164 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A1164 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A1165 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO D 119 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA O -35 " -0.027 2.00e-02 2.50e+03 1.20e-02 3.97e+00 pdb=" N9 DA O -35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA O -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA O -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA O -35 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA O -35 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA O -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA O -35 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA O -35 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA O -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA O -35 " 0.002 2.00e-02 2.50e+03 ... (remaining 3644 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 343 2.61 - 3.18: 21726 3.18 - 3.76: 45918 3.76 - 4.33: 60390 4.33 - 4.90: 90783 Nonbonded interactions: 219160 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.041 2.230 nonbonded pdb=" OG SER C 313 " pdb=" O LYS C 318 " model vdw 2.062 2.440 nonbonded pdb=" O2 DC O 70 " pdb=" N2 DG P -70 " model vdw 2.115 2.496 nonbonded pdb=" O2 DC O -21 " pdb=" N2 DG P 21 " model vdw 2.134 2.496 nonbonded pdb=" O2 DC O -50 " pdb=" N2 DG P 50 " model vdw 2.159 2.496 ... (remaining 219155 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 'G' and (resid 36 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 134)) selection = chain 'K' } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 23 through 101) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.030 Extract box with map and model: 6.990 Check model and map are aligned: 0.440 Set scattering table: 0.250 Process input model: 82.330 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.004 0.055 26475 Z= 0.202 Angle : 0.611 17.267 37008 Z= 0.345 Chirality : 0.036 0.173 4076 Planarity : 0.004 0.068 3647 Dihedral : 23.495 156.538 10692 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.10 % Allowed : 19.33 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2302 helix: 1.96 (0.15), residues: 1279 sheet: 0.32 (0.53), residues: 110 loop : -1.01 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 912 HIS 0.017 0.001 HIS B 43 PHE 0.014 0.001 PHE C 289 TYR 0.028 0.001 TYR L 88 ARG 0.011 0.000 ARG C 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6705 (tpt) cc_final: 0.5145 (tmm) REVERT: B 61 MET cc_start: 0.7266 (mpp) cc_final: 0.6687 (mpp) REVERT: B 306 MET cc_start: 0.9071 (mmm) cc_final: 0.8567 (tpp) REVERT: D 316 MET cc_start: 0.7751 (mmm) cc_final: 0.7473 (mmm) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.3758 time to fit residues: 40.3355 Evaluate side-chains 61 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 67 optimal weight: 20.0000 chunk 132 optimal weight: 0.0870 chunk 104 optimal weight: 50.0000 chunk 203 optimal weight: 10.0000 chunk 78 optimal weight: 0.0270 chunk 123 optimal weight: 20.0000 chunk 151 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 overall best weight: 1.9218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN E 80 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS K 39 HIS K 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26475 Z= 0.148 Angle : 0.505 9.819 37008 Z= 0.291 Chirality : 0.035 0.166 4076 Planarity : 0.004 0.052 3647 Dihedral : 26.029 153.517 5889 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.30 % Allowed : 18.37 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2302 helix: 2.04 (0.15), residues: 1279 sheet: 0.14 (0.50), residues: 113 loop : -0.87 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 912 HIS 0.002 0.000 HIS G 113 PHE 0.012 0.001 PHE C 289 TYR 0.010 0.001 TYR D 356 ARG 0.005 0.000 ARG C 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 62 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6504 (tpt) cc_final: 0.4876 (tmm) REVERT: A 773 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.6318 (pmm) REVERT: A 1194 MET cc_start: 0.3910 (ppp) cc_final: 0.3465 (ppp) REVERT: B 61 MET cc_start: 0.7317 (mpp) cc_final: 0.6626 (tpp) REVERT: B 96 MET cc_start: 0.9209 (mmm) cc_final: 0.8997 (mpp) REVERT: B 305 MET cc_start: 0.8449 (ppp) cc_final: 0.8078 (ppp) REVERT: B 315 MET cc_start: 0.3147 (OUTLIER) cc_final: 0.2536 (pmm) REVERT: C 22 MET cc_start: 0.7805 (mpp) cc_final: 0.7181 (mpp) REVERT: D 316 MET cc_start: 0.7777 (mmm) cc_final: 0.7361 (mmm) REVERT: H 92 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8940 (ptm160) REVERT: K 90 MET cc_start: 0.9139 (mmp) cc_final: 0.8876 (mmm) outliers start: 27 outliers final: 6 residues processed: 82 average time/residue: 0.3703 time to fit residues: 50.5819 Evaluate side-chains 70 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain E residue 22 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 50.0000 chunk 72 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 254 optimal weight: 0.0270 chunk 209 optimal weight: 10.0000 chunk 233 optimal weight: 40.0000 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 0.0770 overall best weight: 3.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 921 GLN ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26475 Z= 0.163 Angle : 0.502 8.376 37008 Z= 0.287 Chirality : 0.035 0.207 4076 Planarity : 0.003 0.044 3647 Dihedral : 25.985 153.502 5889 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.11 % Allowed : 19.23 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2302 helix: 2.02 (0.15), residues: 1287 sheet: 0.03 (0.49), residues: 113 loop : -0.78 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 91 HIS 0.003 0.000 HIS B 43 PHE 0.010 0.001 PHE B 208 TYR 0.010 0.001 TYR D 356 ARG 0.020 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6340 (tpt) cc_final: 0.4731 (tmm) REVERT: A 773 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6303 (pmm) REVERT: A 1194 MET cc_start: 0.3844 (ppp) cc_final: 0.3582 (ppp) REVERT: B 19 ARG cc_start: 0.2749 (OUTLIER) cc_final: 0.1986 (mpp80) REVERT: B 61 MET cc_start: 0.7363 (mpp) cc_final: 0.6733 (tpp) REVERT: B 96 MET cc_start: 0.9217 (mmm) cc_final: 0.9002 (mpp) REVERT: B 306 MET cc_start: 0.8788 (mmt) cc_final: 0.8586 (mmm) REVERT: C 22 MET cc_start: 0.7514 (mpp) cc_final: 0.7190 (mmp) REVERT: D 316 MET cc_start: 0.7983 (mmm) cc_final: 0.7360 (mmm) REVERT: H 92 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8971 (ptm160) REVERT: K 90 MET cc_start: 0.9174 (mmp) cc_final: 0.8915 (mmm) REVERT: K 120 MET cc_start: 0.9039 (mmm) cc_final: 0.8707 (mmt) outliers start: 23 outliers final: 8 residues processed: 81 average time/residue: 0.3708 time to fit residues: 50.1625 Evaluate side-chains 72 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 517 ASN Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain E residue 22 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 112 optimal weight: 0.0470 chunk 158 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 250 optimal weight: 30.0000 chunk 123 optimal weight: 40.0000 chunk 224 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 6.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 ASN ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN E 82 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26475 Z= 0.244 Angle : 0.544 10.534 37008 Z= 0.310 Chirality : 0.036 0.153 4076 Planarity : 0.004 0.042 3647 Dihedral : 26.313 153.038 5889 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.73 % Allowed : 19.47 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2302 helix: 1.93 (0.15), residues: 1295 sheet: 0.10 (0.50), residues: 106 loop : -0.81 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 91 HIS 0.006 0.001 HIS B 43 PHE 0.013 0.001 PHE A 819 TYR 0.024 0.001 TYR B 343 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 61 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6513 (tpt) cc_final: 0.5161 (tmm) REVERT: A 773 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7152 (ppp) REVERT: B 19 ARG cc_start: 0.3149 (OUTLIER) cc_final: 0.1890 (mpp80) REVERT: B 61 MET cc_start: 0.7435 (mpp) cc_final: 0.6910 (tpp) REVERT: B 288 MET cc_start: 0.6712 (tpt) cc_final: 0.6068 (tpt) REVERT: C 22 MET cc_start: 0.7397 (mpp) cc_final: 0.6761 (mpp) REVERT: C 347 MET cc_start: 0.2611 (tpp) cc_final: 0.2178 (tpp) REVERT: D 316 MET cc_start: 0.8252 (mmm) cc_final: 0.8026 (mmm) REVERT: D 375 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.6113 (pm20) REVERT: D 410 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8803 (p0) REVERT: G 90 MET cc_start: 0.9084 (ptp) cc_final: 0.8813 (ptp) REVERT: K 120 MET cc_start: 0.9180 (mmm) cc_final: 0.8952 (mmm) outliers start: 36 outliers final: 21 residues processed: 92 average time/residue: 0.3879 time to fit residues: 57.8119 Evaluate side-chains 82 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 517 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 10.0000 chunk 142 optimal weight: 0.0570 chunk 3 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 127 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 63 optimal weight: 40.0000 overall best weight: 4.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 GLN ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26475 Z= 0.190 Angle : 0.520 8.640 37008 Z= 0.295 Chirality : 0.036 0.166 4076 Planarity : 0.003 0.041 3647 Dihedral : 26.337 152.749 5889 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.73 % Allowed : 19.76 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2302 helix: 2.00 (0.15), residues: 1299 sheet: 0.26 (0.50), residues: 106 loop : -0.71 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 91 HIS 0.003 0.001 HIS B 43 PHE 0.012 0.001 PHE E 78 TYR 0.011 0.001 TYR C 326 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 58 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6550 (tpt) cc_final: 0.5129 (tmm) REVERT: A 773 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7036 (ppp) REVERT: B 19 ARG cc_start: 0.3011 (OUTLIER) cc_final: 0.2626 (mpp80) REVERT: B 61 MET cc_start: 0.7255 (mpp) cc_final: 0.6748 (tpp) REVERT: B 246 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7192 (p) REVERT: C 347 MET cc_start: 0.2816 (tpp) cc_final: 0.2152 (tpp) REVERT: D 316 MET cc_start: 0.8380 (mmm) cc_final: 0.8149 (mmm) REVERT: D 410 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8846 (p0) REVERT: G 90 MET cc_start: 0.9085 (ptp) cc_final: 0.8798 (ptp) REVERT: K 90 MET cc_start: 0.9223 (mmp) cc_final: 0.8961 (mmm) REVERT: K 120 MET cc_start: 0.9199 (mmm) cc_final: 0.8928 (mmm) outliers start: 36 outliers final: 20 residues processed: 89 average time/residue: 0.3594 time to fit residues: 53.8477 Evaluate side-chains 82 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 517 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 50.0000 chunk 225 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 250 optimal weight: 30.0000 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 131 optimal weight: 40.0000 overall best weight: 6.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 26475 Z= 0.273 Angle : 0.567 10.474 37008 Z= 0.320 Chirality : 0.037 0.256 4076 Planarity : 0.004 0.041 3647 Dihedral : 26.555 153.224 5889 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.21 % Allowed : 19.90 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2302 helix: 1.96 (0.15), residues: 1284 sheet: 0.17 (0.51), residues: 102 loop : -0.74 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 782 HIS 0.008 0.001 HIS B 209 PHE 0.011 0.001 PHE E 78 TYR 0.011 0.001 TYR C 326 ARG 0.004 0.000 ARG I 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 57 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6676 (tpt) cc_final: 0.6418 (tpt) REVERT: A 773 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7048 (ppp) REVERT: B 19 ARG cc_start: 0.3021 (OUTLIER) cc_final: 0.2675 (mpp80) REVERT: B 61 MET cc_start: 0.7468 (mpp) cc_final: 0.6990 (tpp) REVERT: B 96 MET cc_start: 0.9193 (mmm) cc_final: 0.8989 (mpp) REVERT: C 22 MET cc_start: 0.7086 (mpp) cc_final: 0.6444 (mmp) REVERT: C 347 MET cc_start: 0.3088 (tpp) cc_final: 0.2296 (tpp) REVERT: D 410 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8860 (p0) REVERT: I 71 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.9043 (ttp80) REVERT: G 90 MET cc_start: 0.9097 (ptp) cc_final: 0.8840 (ptp) REVERT: K 90 MET cc_start: 0.9196 (mmp) cc_final: 0.8915 (mmm) REVERT: K 120 MET cc_start: 0.9258 (mmm) cc_final: 0.8978 (mmm) outliers start: 46 outliers final: 26 residues processed: 96 average time/residue: 0.3819 time to fit residues: 59.9986 Evaluate side-chains 87 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 57 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 517 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 7.9990 chunk 28 optimal weight: 40.0000 chunk 142 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26475 Z= 0.240 Angle : 0.555 10.303 37008 Z= 0.313 Chirality : 0.036 0.180 4076 Planarity : 0.004 0.041 3647 Dihedral : 26.660 153.080 5889 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.63 % Allowed : 20.53 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2302 helix: 1.97 (0.15), residues: 1282 sheet: 0.06 (0.52), residues: 101 loop : -0.71 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 91 HIS 0.004 0.001 HIS B 209 PHE 0.011 0.001 PHE B 208 TYR 0.013 0.001 TYR L 88 ARG 0.008 0.000 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 57 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6638 (tpt) cc_final: 0.6379 (tpt) REVERT: A 773 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7029 (ppp) REVERT: B 19 ARG cc_start: 0.3144 (OUTLIER) cc_final: 0.2680 (mpp80) REVERT: B 61 MET cc_start: 0.7554 (mpp) cc_final: 0.7055 (tpp) REVERT: B 204 MET cc_start: -0.1719 (mmm) cc_final: -0.1944 (mmm) REVERT: B 288 MET cc_start: 0.6306 (tpt) cc_final: 0.5862 (tpt) REVERT: B 306 MET cc_start: 0.8923 (mmm) cc_final: 0.8611 (mmm) REVERT: C 22 MET cc_start: 0.7049 (mpp) cc_final: 0.6676 (mmp) REVERT: C 347 MET cc_start: 0.3241 (tpp) cc_final: 0.2309 (tpp) REVERT: D 316 MET cc_start: 0.8644 (mmm) cc_final: 0.8013 (mmm) REVERT: D 410 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8901 (p0) REVERT: I 71 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.9049 (ttp80) REVERT: G 90 MET cc_start: 0.9093 (ptp) cc_final: 0.8829 (ptp) REVERT: K 120 MET cc_start: 0.9246 (mmm) cc_final: 0.8959 (mmm) outliers start: 34 outliers final: 27 residues processed: 86 average time/residue: 0.3892 time to fit residues: 54.3729 Evaluate side-chains 87 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 56 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 517 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 50.0000 chunk 49 optimal weight: 50.0000 chunk 48 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26475 Z= 0.199 Angle : 0.540 11.354 37008 Z= 0.304 Chirality : 0.036 0.181 4076 Planarity : 0.003 0.041 3647 Dihedral : 26.622 152.512 5889 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.63 % Allowed : 20.72 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2302 helix: 2.04 (0.15), residues: 1278 sheet: -0.00 (0.51), residues: 105 loop : -0.68 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 91 HIS 0.003 0.001 HIS B 209 PHE 0.011 0.001 PHE B 208 TYR 0.012 0.001 TYR C 326 ARG 0.012 0.000 ARG M 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 58 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6320 (tpt) cc_final: 0.6071 (tpt) REVERT: A 773 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7066 (ppp) REVERT: B 19 ARG cc_start: 0.3371 (OUTLIER) cc_final: 0.2017 (mpp80) REVERT: B 61 MET cc_start: 0.7650 (mpp) cc_final: 0.7102 (tpp) REVERT: B 288 MET cc_start: 0.6545 (tpt) cc_final: 0.6159 (tpt) REVERT: B 305 MET cc_start: 0.8634 (ppp) cc_final: 0.8164 (ppp) REVERT: C 22 MET cc_start: 0.7058 (mpp) cc_final: 0.6721 (mmp) REVERT: C 256 MET cc_start: 0.8832 (ptp) cc_final: 0.8299 (pmm) REVERT: C 347 MET cc_start: 0.3001 (tpp) cc_final: 0.2096 (tpp) REVERT: D 316 MET cc_start: 0.8751 (mmm) cc_final: 0.8133 (mmm) REVERT: D 410 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8923 (p0) REVERT: G 90 MET cc_start: 0.9094 (ptp) cc_final: 0.8828 (ptp) REVERT: K 120 MET cc_start: 0.9247 (mmm) cc_final: 0.8961 (mmm) outliers start: 34 outliers final: 27 residues processed: 87 average time/residue: 0.3597 time to fit residues: 52.8758 Evaluate side-chains 87 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 57 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 517 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 50.0000 chunk 182 optimal weight: 8.9990 chunk 71 optimal weight: 50.0000 chunk 210 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 231 optimal weight: 0.0060 overall best weight: 6.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26475 Z= 0.237 Angle : 0.566 11.965 37008 Z= 0.317 Chirality : 0.036 0.193 4076 Planarity : 0.004 0.041 3647 Dihedral : 26.733 152.038 5889 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.68 % Allowed : 20.91 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2302 helix: 1.98 (0.15), residues: 1275 sheet: -0.02 (0.51), residues: 105 loop : -0.68 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 91 HIS 0.003 0.001 HIS B 209 PHE 0.012 0.001 PHE B 160 TYR 0.012 0.001 TYR L 88 ARG 0.005 0.000 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 55 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: 0.6553 (tpt) cc_final: 0.6262 (tpt) REVERT: A 773 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.6979 (ppp) REVERT: B 19 ARG cc_start: 0.3575 (OUTLIER) cc_final: 0.1887 (mpp80) REVERT: B 47 MET cc_start: 0.2436 (pmm) cc_final: 0.2158 (pmm) REVERT: B 61 MET cc_start: 0.7549 (mpp) cc_final: 0.6998 (tpp) REVERT: B 288 MET cc_start: 0.6558 (tpt) cc_final: 0.6184 (tpt) REVERT: B 305 MET cc_start: 0.8491 (ppp) cc_final: 0.7868 (ppp) REVERT: B 306 MET cc_start: 0.8814 (mmm) cc_final: 0.8568 (mmm) REVERT: C 22 MET cc_start: 0.7116 (mpp) cc_final: 0.6868 (mmp) REVERT: C 347 MET cc_start: 0.2987 (tpp) cc_final: 0.2074 (tpp) REVERT: D 316 MET cc_start: 0.8790 (mmm) cc_final: 0.8180 (mmm) REVERT: D 410 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8936 (p0) REVERT: I 71 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.9026 (ttp80) REVERT: N 56 MET cc_start: 0.9135 (ppp) cc_final: 0.8598 (ppp) REVERT: G 90 MET cc_start: 0.9102 (ptp) cc_final: 0.8843 (ptp) REVERT: K 90 MET cc_start: 0.9228 (mmp) cc_final: 0.8957 (mmm) REVERT: K 120 MET cc_start: 0.9248 (mmm) cc_final: 0.8935 (mmm) outliers start: 35 outliers final: 29 residues processed: 85 average time/residue: 0.3724 time to fit residues: 52.5448 Evaluate side-chains 88 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 55 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 517 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 258 optimal weight: 0.6980 chunk 237 optimal weight: 50.0000 chunk 205 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26475 Z= 0.158 Angle : 0.535 13.164 37008 Z= 0.300 Chirality : 0.036 0.201 4076 Planarity : 0.003 0.041 3647 Dihedral : 26.572 150.593 5889 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.30 % Allowed : 21.49 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2302 helix: 2.09 (0.15), residues: 1281 sheet: 0.01 (0.51), residues: 106 loop : -0.63 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 91 HIS 0.003 0.001 HIS A1293 PHE 0.011 0.001 PHE B 208 TYR 0.019 0.001 TYR L 88 ARG 0.005 0.000 ARG J 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 56 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7069 (ppp) REVERT: B 19 ARG cc_start: 0.3648 (OUTLIER) cc_final: 0.2219 (mpp80) REVERT: B 47 MET cc_start: 0.2065 (pmm) cc_final: 0.1748 (pmm) REVERT: B 61 MET cc_start: 0.7549 (mpp) cc_final: 0.6548 (mpp) REVERT: B 305 MET cc_start: 0.8584 (ppp) cc_final: 0.8106 (ppp) REVERT: C 256 MET cc_start: 0.8837 (ptp) cc_final: 0.8342 (pmm) REVERT: C 347 MET cc_start: 0.2917 (tpp) cc_final: 0.1968 (tpp) REVERT: D 316 MET cc_start: 0.8762 (mmm) cc_final: 0.8133 (mmm) REVERT: D 410 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8910 (p0) REVERT: N 56 MET cc_start: 0.9174 (ppp) cc_final: 0.8770 (ppp) REVERT: K 90 MET cc_start: 0.9223 (mmp) cc_final: 0.8930 (mmm) REVERT: K 120 MET cc_start: 0.9151 (mmm) cc_final: 0.8840 (mmm) outliers start: 27 outliers final: 22 residues processed: 80 average time/residue: 0.3657 time to fit residues: 49.4366 Evaluate side-chains 81 residues out of total 2081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 56 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 517 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 92 ARG Chi-restraints excluded: chain I residue 74 LYS Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 30 optimal weight: 40.0000 chunk 57 optimal weight: 0.7980 chunk 205 optimal weight: 10.0000 chunk 86 optimal weight: 50.0000 chunk 211 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.034698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.022076 restraints weight = 394882.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.022347 restraints weight = 276358.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.022535 restraints weight = 217375.485| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26475 Z= 0.213 Angle : 0.560 13.127 37008 Z= 0.313 Chirality : 0.036 0.192 4076 Planarity : 0.004 0.041 3647 Dihedral : 26.606 150.370 5889 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.30 % Allowed : 21.54 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2302 helix: 2.11 (0.15), residues: 1271 sheet: 0.07 (0.52), residues: 106 loop : -0.63 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 365 HIS 0.018 0.001 HIS C 18 PHE 0.011 0.001 PHE B 208 TYR 0.016 0.001 TYR L 88 ARG 0.005 0.000 ARG J 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3486.27 seconds wall clock time: 65 minutes 28.94 seconds (3928.94 seconds total)