Starting phenix.real_space_refine on Sat Aug 10 16:29:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/08_2024/7kim_22887.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/08_2024/7kim_22887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/08_2024/7kim_22887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/08_2024/7kim_22887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/08_2024/7kim_22887.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/08_2024/7kim_22887.cif" } resolution = 3.38 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= 0.002 sd= 1.022 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 2 6.06 5 P 89 5.49 5 Mg 1 5.21 5 S 107 5.16 5 C 18252 2.51 5 N 5286 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 551": "OD1" <-> "OD2" Residue "C GLU 732": "OE1" <-> "OE2" Residue "C ARG 787": "NH1" <-> "NH2" Residue "C ARG 791": "NH1" <-> "NH2" Residue "C ASP 800": "OD1" <-> "OD2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "C GLU 1087": "OE1" <-> "OE2" Residue "C TYR 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "D PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D GLU 665": "OE1" <-> "OE2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ASP 862": "OD1" <-> "OD2" Residue "D ARG 876": "NH1" <-> "NH2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "D GLU 948": "OE1" <-> "OE2" Residue "D TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1041": "NH1" <-> "NH2" Residue "D ARG 1054": "NH1" <-> "NH2" Residue "D GLU 1129": "OE1" <-> "OE2" Residue "D GLU 1155": "OE1" <-> "OE2" Residue "D ASP 1235": "OD1" <-> "OD2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "M TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 31": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29573 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8606 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 9914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9914 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "F" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2544 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 880 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1039 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 2 Chain: "O" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 920 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain: "P" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 922 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "Z" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19155 SG CYS D 891 114.936 131.607 114.993 1.00137.02 S ATOM 19722 SG CYS D 968 111.195 131.308 112.527 1.00127.78 S ATOM 19764 SG CYS D 975 112.292 129.853 115.048 1.00125.21 S ATOM 19782 SG CYS D 978 111.876 132.982 116.082 1.00117.11 S ATOM 12593 SG CYS D 60 84.017 83.089 77.791 1.00181.94 S ATOM 12611 SG CYS D 62 82.559 82.774 74.039 1.00177.55 S ATOM 12720 SG CYS D 75 86.363 82.884 74.486 1.00185.09 S ATOM 12746 SG CYS D 78 84.844 85.594 75.414 1.00182.67 S ATOM 29206 SG CYS Z 43 73.204 59.311 120.596 1.00158.72 S ATOM 29034 SG CYS Z 20 73.958 63.141 118.748 1.00163.44 S ATOM 29225 SG CYS Z 46 70.806 62.758 121.419 1.00154.31 S ATOM 29277 SG CYS Z 52 70.292 61.771 115.141 1.00154.44 S ATOM 29034 SG CYS Z 20 73.958 63.141 118.748 1.00163.44 S ATOM 29206 SG CYS Z 43 73.204 59.311 120.596 1.00158.72 S Time building chain proxies: 14.96, per 1000 atoms: 0.51 Number of scatterers: 29573 At special positions: 0 Unit cell: (140.8, 188.1, 199.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Fe 4 26.01 S 107 16.00 P 89 15.00 Mg 1 11.99 O 5832 8.00 N 5286 7.00 C 18252 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: 11.35 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 Z 101 " pdb="FE4 SF4 Z 101 " - pdb=" SG CYS Z 20 " pdb="FE1 SF4 Z 101 " - pdb=" SG CYS Z 43 " pdb="FE2 SF4 Z 101 " - pdb=" SG CYS Z 46 " pdb="FE3 SF4 Z 101 " - pdb=" SG CYS Z 52 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " Number of angles added : 12 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6582 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 47 sheets defined 41.5% alpha, 12.0% beta 44 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 9.79 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.120A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.537A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 4.110A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.870A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.981A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.642A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.893A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 4.048A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 589 through 593 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 958 removed outlier: 3.675A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG C 958 " --> pdb=" O TRP C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.898A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1041 removed outlier: 3.926A pdb=" N LYS C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.750A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.532A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.541A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.777A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.504A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 186 removed outlier: 4.063A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.974A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.361A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.548A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.016A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 393 through 397 removed outlier: 4.281A pdb=" N ARG D 397 " --> pdb=" O PRO D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 407 through 411 removed outlier: 4.041A pdb=" N GLN D 410 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY D 411 " --> pdb=" O GLY D 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 407 through 411' Processing helix chain 'D' and resid 444 through 452 removed outlier: 4.114A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.484A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.530A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 Processing helix chain 'D' and resid 732 through 736 removed outlier: 3.775A pdb=" N VAL D 736 " --> pdb=" O MET D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.832A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 4.048A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.101A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 975 through 980 removed outlier: 3.709A pdb=" N TYR D 979 " --> pdb=" O CYS D 975 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY D 980 " --> pdb=" O ALA D 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 975 through 980' Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1036 removed outlier: 3.624A pdb=" N VAL D1031 " --> pdb=" O GLY D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1144 removed outlier: 3.588A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 4.059A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D1136 " --> pdb=" O ILE D1132 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 3.989A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1193 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.662A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D1236 " --> pdb=" O VAL D1232 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE D1238 " --> pdb=" O THR D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1254 removed outlier: 3.825A pdb=" N VAL D1252 " --> pdb=" O LEU D1248 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D1253 " --> pdb=" O LYS D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1280 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.796A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 208 through 223 removed outlier: 4.340A pdb=" N LEU F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP F 218 " --> pdb=" O GLN F 214 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 242 through 268 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.344A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.928A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 5.037A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 418 removed outlier: 3.705A pdb=" N ARG F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 437 removed outlier: 3.566A pdb=" N ASP F 437 " --> pdb=" O GLN F 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 434 through 437' Processing helix chain 'F' and resid 448 through 465 Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 516 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 50 through 57 removed outlier: 4.105A pdb=" N GLU M 54 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR M 55 " --> pdb=" O GLU M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 4.019A pdb=" N ALA M 76 " --> pdb=" O GLN M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 97 removed outlier: 3.534A pdb=" N LEU M 96 " --> pdb=" O ASN M 92 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA M 97 " --> pdb=" O LEU M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 105 removed outlier: 3.642A pdb=" N ALA M 105 " --> pdb=" O VAL M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 143 Processing helix chain 'M' and resid 150 through 157 Processing helix chain 'Z' and resid 24 through 30 Processing helix chain 'Z' and resid 36 through 43 removed outlier: 3.592A pdb=" N CYS Z 43 " --> pdb=" O ALA Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 46 No H-bonds generated for 'chain 'Z' and resid 44 through 46' Processing helix chain 'Z' and resid 48 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.990A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.990A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.539A pdb=" N VAL A 93 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 136 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.600A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.540A pdb=" N VAL B 196 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 177 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.782A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 50 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.802A pdb=" N VAL B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.776A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.592A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.592A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 147 " --> pdb=" O ARG M 47 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG M 47 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 7.290A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 204 removed outlier: 3.693A pdb=" N PHE C 214 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 204 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AB9, first strand: chain 'C' and resid 519 through 520 Processing sheet with id=AC1, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.687A pdb=" N VAL C 561 " --> pdb=" O GLU C 569 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 626 through 627 removed outlier: 3.790A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.744A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.791A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.579A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C1026 " --> pdb=" O VAL C 721 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 749 through 750 Processing sheet with id=AC8, first strand: chain 'C' and resid 753 through 759 removed outlier: 3.819A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 761 through 762 removed outlier: 3.631A pdb=" N GLY C 765 " --> pdb=" O THR C 762 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.546A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.754A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.546A pdb=" N HIS C1042 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 544 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.546A pdb=" N HIS C1042 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1067 through 1068 removed outlier: 3.922A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1135 through 1138 Processing sheet with id=AD7, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AD8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AD9, first strand: chain 'D' and resid 233 through 235 removed outlier: 4.300A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 421 through 422 removed outlier: 5.993A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER J 9 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU F 440 " --> pdb=" O LEU J 6 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY J 8 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 7.108A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1076 removed outlier: 3.701A pdb=" N THR D1065 " --> pdb=" O ARG D1054 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1061 through 1062 Processing sheet with id=AE6, first strand: chain 'D' and resid 1085 through 1086 removed outlier: 4.494A pdb=" N ARG D1085 " --> pdb=" O GLU D1113 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 3.568A pdb=" N ARG D1204 " --> pdb=" O THR D1166 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.603A pdb=" N ALA D1271 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 107 " --> pdb=" O ALA D1271 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D1273 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AF1, first strand: chain 'M' and resid 15 through 18 Processing sheet with id=AF2, first strand: chain 'M' and resid 26 through 27 1164 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 13.02 Time building geometry restraints manager: 12.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 12405 1.42 - 1.64: 17662 1.64 - 1.86: 179 1.86 - 2.07: 0 2.07 - 2.29: 12 Bond restraints: 30258 Sorted by residual: bond pdb=" C SER C 973 " pdb=" N THR C 974 " ideal model delta sigma weight residual 1.333 1.264 0.069 1.61e-02 3.86e+03 1.85e+01 bond pdb=" CA THR D 967 " pdb=" C THR D 967 " ideal model delta sigma weight residual 1.523 1.490 0.033 1.28e-02 6.10e+03 6.67e+00 bond pdb=" CA THR C 659 " pdb=" CB THR C 659 " ideal model delta sigma weight residual 1.525 1.489 0.036 1.47e-02 4.63e+03 6.02e+00 bond pdb=" CA CYS D 978 " pdb=" CB CYS D 978 " ideal model delta sigma weight residual 1.529 1.490 0.039 1.62e-02 3.81e+03 5.77e+00 bond pdb=" C ASP A 90 " pdb=" N GLU A 91 " ideal model delta sigma weight residual 1.339 1.207 0.132 5.57e-02 3.22e+02 5.64e+00 ... (remaining 30253 not shown) Histogram of bond angle deviations from ideal: 73.30 - 87.43: 12 87.43 - 101.56: 162 101.56 - 115.69: 20299 115.69 - 129.81: 20735 129.81 - 143.94: 165 Bond angle restraints: 41373 Sorted by residual: angle pdb=" N PRO Z 11 " pdb=" CA PRO Z 11 " pdb=" CB PRO Z 11 " ideal model delta sigma weight residual 103.25 112.04 -8.79 1.05e+00 9.07e-01 7.01e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta sigma weight residual 127.00 143.94 -16.94 2.40e+00 1.74e-01 4.98e+01 angle pdb=" C VAL D 965 " pdb=" N LEU D 966 " pdb=" CA LEU D 966 " ideal model delta sigma weight residual 121.54 134.70 -13.16 1.91e+00 2.74e-01 4.74e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CD PRO D 835 " ideal model delta sigma weight residual 120.60 106.66 13.94 2.20e+00 2.07e-01 4.01e+01 angle pdb=" N ALA M 148 " pdb=" CA ALA M 148 " pdb=" C ALA M 148 " ideal model delta sigma weight residual 110.80 120.97 -10.17 2.13e+00 2.20e-01 2.28e+01 ... (remaining 41368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.31: 17165 32.31 - 64.61: 1048 64.61 - 96.92: 61 96.92 - 129.22: 0 129.22 - 161.53: 1 Dihedral angle restraints: 18275 sinusoidal: 8048 harmonic: 10227 Sorted by residual: dihedral pdb=" CA ASP M 147 " pdb=" C ASP M 147 " pdb=" N ALA M 148 " pdb=" CA ALA M 148 " ideal model delta harmonic sigma weight residual -180.00 -129.14 -50.86 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA THR D1173 " pdb=" C THR D1173 " pdb=" N GLU D1174 " pdb=" CA GLU D1174 " ideal model delta harmonic sigma weight residual 180.00 143.67 36.33 0 5.00e+00 4.00e-02 5.28e+01 dihedral pdb=" CA VAL E 79 " pdb=" C VAL E 79 " pdb=" N GLY E 80 " pdb=" CA GLY E 80 " ideal model delta harmonic sigma weight residual 180.00 146.22 33.78 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 18272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3646 0.061 - 0.123: 950 0.123 - 0.184: 106 0.184 - 0.245: 7 0.245 - 0.307: 4 Chirality restraints: 4713 Sorted by residual: chirality pdb=" CB ILE M 27 " pdb=" CA ILE M 27 " pdb=" CG1 ILE M 27 " pdb=" CG2 ILE M 27 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA PRO Z 11 " pdb=" N PRO Z 11 " pdb=" C PRO Z 11 " pdb=" CB PRO Z 11 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA GLN D 657 " pdb=" N GLN D 657 " pdb=" C GLN D 657 " pdb=" CB GLN D 657 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4710 not shown) Planarity restraints: 5124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 444 " -0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO C 445 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 975 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C CYS D 975 " -0.060 2.00e-02 2.50e+03 pdb=" O CYS D 975 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA D 976 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 773 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO C 774 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 774 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 774 " -0.045 5.00e-02 4.00e+02 ... (remaining 5121 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 7 2.17 - 2.85: 10505 2.85 - 3.53: 42061 3.53 - 4.22: 67830 4.22 - 4.90: 114092 Nonbonded interactions: 234495 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb=" OD2 ASP D 539 " model vdw 1.482 3.040 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.019 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.059 2.170 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D2002 " model vdw 2.114 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.143 2.170 ... (remaining 234490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 2 through 226) } 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=0.50 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: 1.610 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: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 90.580 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.132 30258 Z= 0.545 Angle : 0.878 16.942 41373 Z= 0.497 Chirality : 0.053 0.307 4713 Planarity : 0.007 0.097 5124 Dihedral : 18.440 161.530 11693 Min Nonbonded Distance : 1.482 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.28 % Favored : 92.61 % Rotamer: Outliers : 7.44 % Allowed : 15.25 % Favored : 77.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.59 (0.13), residues: 3546 helix: -0.95 (0.12), residues: 1373 sheet: -2.30 (0.25), residues: 400 loop : -2.20 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 223 HIS 0.011 0.001 HIS F 516 PHE 0.021 0.002 PHE C 906 TYR 0.022 0.002 TYR A 168 ARG 0.006 0.001 ARG D1054 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 142 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.7598 (p90) REVERT: B 197 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: C 127 MET cc_start: 0.8964 (pmm) cc_final: 0.8667 (pmm) REVERT: C 584 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8650 (ptt-90) REVERT: C 611 MET cc_start: 0.8375 (ptp) cc_final: 0.8066 (ptp) REVERT: C 661 MET cc_start: 0.8613 (tpp) cc_final: 0.8257 (tpp) REVERT: C 664 ASN cc_start: 0.9298 (OUTLIER) cc_final: 0.8928 (p0) REVERT: C 730 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.9022 (p0) REVERT: C 1035 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7212 (m-70) REVERT: C 1051 MET cc_start: 0.9009 (mmm) cc_final: 0.8679 (mmm) REVERT: C 1104 GLU cc_start: 0.8647 (pp20) cc_final: 0.8398 (pp20) REVERT: D 327 MET cc_start: 0.8799 (tpt) cc_final: 0.8467 (tpt) REVERT: D 379 ASP cc_start: 0.8523 (m-30) cc_final: 0.8142 (m-30) REVERT: D 417 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8321 (mt) REVERT: D 663 MET cc_start: 0.8945 (mmm) cc_final: 0.8715 (mmm) REVERT: D 862 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8186 (p0) REVERT: D 879 ASP cc_start: 0.8404 (m-30) cc_final: 0.8167 (m-30) REVERT: D 1165 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8685 (p) REVERT: E 66 ASP cc_start: 0.9306 (t70) cc_final: 0.8616 (t0) REVERT: E 102 ASP cc_start: 0.9328 (t0) cc_final: 0.9040 (t0) REVERT: F 359 MET cc_start: 0.9081 (tmm) cc_final: 0.8793 (tmm) REVERT: F 458 ASP cc_start: 0.9046 (m-30) cc_final: 0.8715 (m-30) REVERT: J 16 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8498 (p90) REVERT: J 19 ASP cc_start: 0.8360 (t70) cc_final: 0.8037 (t0) REVERT: J 64 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9077 (mt) REVERT: J 84 MET cc_start: 0.8346 (ppp) cc_final: 0.7834 (ppp) REVERT: M 41 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7906 (tm-30) REVERT: M 43 ASP cc_start: 0.8023 (t70) cc_final: 0.7637 (t0) REVERT: M 44 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8911 (pt) outliers start: 221 outliers final: 102 residues processed: 351 average time/residue: 0.3273 time to fit residues: 196.6381 Evaluate side-chains 243 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 129 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 664 ASN Chi-restraints excluded: chain C residue 730 ASN Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1035 HIS Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 213 ARG Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain Z residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 185 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 283 optimal weight: 0.0670 chunk 109 optimal weight: 0.8980 chunk 172 optimal weight: 10.0000 chunk 211 optimal weight: 0.7980 chunk 328 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS C 443 ASN C 507 ASN C1035 HIS ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN D 854 HIS J 21 ASN J 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 30258 Z= 0.164 Angle : 0.587 13.613 41373 Z= 0.311 Chirality : 0.042 0.182 4713 Planarity : 0.005 0.066 5124 Dihedral : 17.776 162.294 5073 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 4.01 % Allowed : 17.10 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.57 (0.14), residues: 3546 helix: 0.32 (0.14), residues: 1386 sheet: -2.10 (0.25), residues: 409 loop : -1.93 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 723 HIS 0.003 0.001 HIS C 941 PHE 0.012 0.001 PHE D1186 TYR 0.017 0.001 TYR A 168 ARG 0.006 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 154 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.7227 (p90) REVERT: B 39 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8578 (ttt-90) REVERT: C 148 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8609 (mppt) REVERT: C 263 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8724 (pp20) REVERT: C 611 MET cc_start: 0.8261 (ptp) cc_final: 0.7855 (ptp) REVERT: C 630 MET cc_start: 0.8676 (ttp) cc_final: 0.8280 (tmm) REVERT: C 730 ASN cc_start: 0.9242 (OUTLIER) cc_final: 0.9024 (p0) REVERT: C 1051 MET cc_start: 0.8996 (mmm) cc_final: 0.8678 (mmm) REVERT: C 1104 GLU cc_start: 0.8609 (pp20) cc_final: 0.8325 (pp20) REVERT: D 256 MET cc_start: 0.7209 (tmm) cc_final: 0.6377 (tmt) REVERT: D 379 ASP cc_start: 0.8451 (m-30) cc_final: 0.7982 (m-30) REVERT: D 862 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8179 (p0) REVERT: D 991 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8624 (mm) REVERT: D 1062 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: E 30 ASP cc_start: 0.8396 (t0) cc_final: 0.8184 (t0) REVERT: E 35 ILE cc_start: 0.9559 (tt) cc_final: 0.9323 (tt) REVERT: E 66 ASP cc_start: 0.9248 (t70) cc_final: 0.8655 (t0) REVERT: E 102 ASP cc_start: 0.9303 (t0) cc_final: 0.9050 (t0) REVERT: F 359 MET cc_start: 0.9131 (tmm) cc_final: 0.8776 (tmm) REVERT: F 458 ASP cc_start: 0.9084 (m-30) cc_final: 0.8702 (m-30) REVERT: J 16 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8593 (p90) REVERT: J 19 ASP cc_start: 0.8406 (t70) cc_final: 0.8024 (t0) REVERT: J 84 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8025 (ppp) REVERT: M 41 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7916 (tm-30) REVERT: M 43 ASP cc_start: 0.8338 (t70) cc_final: 0.7999 (t0) REVERT: Z 31 ASP cc_start: 0.8665 (p0) cc_final: 0.8353 (p0) outliers start: 119 outliers final: 67 residues processed: 265 average time/residue: 0.3432 time to fit residues: 157.0537 Evaluate side-chains 210 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 133 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 730 ASN Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain Z residue 38 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 223 optimal weight: 0.4980 chunk 90 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 355 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 326 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 264 optimal weight: 20.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS C 141 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 21 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30258 Z= 0.172 Angle : 0.557 12.006 41373 Z= 0.293 Chirality : 0.041 0.232 4713 Planarity : 0.005 0.132 5124 Dihedral : 17.341 162.308 4978 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 3.37 % Allowed : 17.91 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.09 (0.14), residues: 3546 helix: 0.86 (0.14), residues: 1383 sheet: -1.84 (0.25), residues: 416 loop : -1.77 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 223 HIS 0.003 0.001 HIS D 854 PHE 0.006 0.001 PHE C 153 TYR 0.015 0.001 TYR A 168 ARG 0.014 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 146 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.7038 (p90) REVERT: A 194 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9053 (tt) REVERT: B 39 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8650 (ttt-90) REVERT: C 127 MET cc_start: 0.8793 (pmm) cc_final: 0.8529 (pmm) REVERT: C 535 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8914 (mp0) REVERT: C 630 MET cc_start: 0.8736 (ttp) cc_final: 0.7905 (tmm) REVERT: C 661 MET cc_start: 0.8013 (tpp) cc_final: 0.7794 (tpp) REVERT: C 723 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8964 (mm) REVERT: C 1051 MET cc_start: 0.9062 (mmm) cc_final: 0.8757 (mmm) REVERT: C 1104 GLU cc_start: 0.8615 (pp20) cc_final: 0.8328 (pp20) REVERT: D 256 MET cc_start: 0.7196 (tmm) cc_final: 0.6194 (tmt) REVERT: D 379 ASP cc_start: 0.8454 (m-30) cc_final: 0.8024 (m-30) REVERT: D 862 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8195 (p0) REVERT: D 953 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9149 (pp) REVERT: D 1059 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7328 (pp20) REVERT: E 30 ASP cc_start: 0.8437 (t0) cc_final: 0.8157 (t0) REVERT: E 35 ILE cc_start: 0.9563 (tt) cc_final: 0.9349 (tt) REVERT: E 66 ASP cc_start: 0.9259 (t70) cc_final: 0.8662 (t0) REVERT: E 102 ASP cc_start: 0.9293 (t0) cc_final: 0.9046 (t0) REVERT: F 359 MET cc_start: 0.9111 (tmm) cc_final: 0.8733 (tmm) REVERT: F 458 ASP cc_start: 0.9069 (m-30) cc_final: 0.8689 (m-30) REVERT: J 16 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8692 (p90) REVERT: J 19 ASP cc_start: 0.8429 (t70) cc_final: 0.8060 (t0) REVERT: J 84 MET cc_start: 0.8352 (ppp) cc_final: 0.7974 (ppp) REVERT: M 41 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7826 (tm-30) REVERT: M 43 ASP cc_start: 0.8484 (t70) cc_final: 0.8132 (t0) REVERT: Z 31 ASP cc_start: 0.8658 (p0) cc_final: 0.8363 (p0) outliers start: 100 outliers final: 62 residues processed: 233 average time/residue: 0.3418 time to fit residues: 138.5074 Evaluate side-chains 206 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 135 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1059 GLU Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 38 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 221 optimal weight: 0.0010 chunk 330 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 313 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 overall best weight: 5.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 610 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN D 687 GLN E 70 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 30258 Z= 0.424 Angle : 0.665 9.020 41373 Z= 0.348 Chirality : 0.043 0.214 4713 Planarity : 0.005 0.066 5124 Dihedral : 17.312 163.390 4958 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.47 % Favored : 92.44 % Rotamer: Outliers : 4.78 % Allowed : 17.77 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.06 (0.14), residues: 3546 helix: 0.90 (0.14), residues: 1388 sheet: -1.98 (0.25), residues: 438 loop : -1.71 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 66 HIS 0.007 0.001 HIS F 516 PHE 0.012 0.001 PHE C 373 TYR 0.025 0.002 TYR M 11 ARG 0.009 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 129 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.7759 (p90) REVERT: A 194 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9060 (tt) REVERT: B 39 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8768 (ttt-90) REVERT: B 188 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8652 (m-30) REVERT: C 124 ASP cc_start: 0.9274 (OUTLIER) cc_final: 0.9013 (p0) REVERT: C 225 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7544 (ptm160) REVERT: C 535 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8984 (mp0) REVERT: C 611 MET cc_start: 0.8348 (ptp) cc_final: 0.7930 (ptp) REVERT: C 630 MET cc_start: 0.8953 (ttp) cc_final: 0.7816 (tmm) REVERT: C 661 MET cc_start: 0.8020 (tpp) cc_final: 0.7785 (tpp) REVERT: C 1104 GLU cc_start: 0.8702 (pp20) cc_final: 0.8437 (pp20) REVERT: D 256 MET cc_start: 0.7166 (tmm) cc_final: 0.6043 (tmt) REVERT: D 379 ASP cc_start: 0.8563 (m-30) cc_final: 0.8156 (m-30) REVERT: D 862 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8175 (p0) REVERT: D 953 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9155 (mm) REVERT: D 1025 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6801 (p) REVERT: D 1062 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: E 30 ASP cc_start: 0.8554 (t0) cc_final: 0.8272 (t0) REVERT: E 66 ASP cc_start: 0.9267 (t70) cc_final: 0.8664 (t0) REVERT: F 359 MET cc_start: 0.9119 (tmm) cc_final: 0.8738 (tmm) REVERT: F 458 ASP cc_start: 0.9068 (m-30) cc_final: 0.8710 (m-30) REVERT: J 16 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8784 (p90) REVERT: J 19 ASP cc_start: 0.8443 (t70) cc_final: 0.8093 (t0) REVERT: J 64 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8897 (mt) REVERT: J 84 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7922 (ppp) REVERT: M 41 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7862 (tm-30) REVERT: M 43 ASP cc_start: 0.8470 (t70) cc_final: 0.8087 (t0) REVERT: M 149 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8126 (ptmm) REVERT: Z 31 ASP cc_start: 0.8623 (p0) cc_final: 0.8350 (p0) outliers start: 142 outliers final: 90 residues processed: 258 average time/residue: 0.3446 time to fit residues: 152.7237 Evaluate side-chains 230 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 125 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1086 GLN Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain Z residue 38 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 30.0000 chunk 198 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 chunk 241 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30258 Z= 0.211 Angle : 0.564 9.690 41373 Z= 0.296 Chirality : 0.041 0.165 4713 Planarity : 0.004 0.089 5124 Dihedral : 17.191 167.485 4955 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 4.14 % Allowed : 18.71 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3546 helix: 1.14 (0.14), residues: 1389 sheet: -1.75 (0.25), residues: 409 loop : -1.64 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 223 HIS 0.003 0.001 HIS D 854 PHE 0.007 0.001 PHE C 61 TYR 0.015 0.001 TYR A 168 ARG 0.009 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 137 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.7565 (p90) REVERT: A 194 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9041 (tt) REVERT: B 39 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8673 (ttt-90) REVERT: B 188 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8644 (m-30) REVERT: C 127 MET cc_start: 0.8706 (pmm) cc_final: 0.8466 (pmm) REVERT: C 225 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7412 (ptm160) REVERT: C 263 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8698 (pp20) REVERT: C 402 GLU cc_start: 0.9552 (OUTLIER) cc_final: 0.9289 (pp20) REVERT: C 535 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8950 (mp0) REVERT: C 630 MET cc_start: 0.8819 (ttp) cc_final: 0.7878 (tmm) REVERT: C 1104 GLU cc_start: 0.8663 (pp20) cc_final: 0.8366 (pp20) REVERT: D 256 MET cc_start: 0.7218 (tmm) cc_final: 0.6039 (tmt) REVERT: D 310 MET cc_start: 0.8223 (mmm) cc_final: 0.8013 (mmm) REVERT: D 379 ASP cc_start: 0.8465 (m-30) cc_final: 0.7980 (m-30) REVERT: D 862 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8220 (p0) REVERT: D 953 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9167 (pp) REVERT: D 1025 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6888 (p) REVERT: D 1062 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: E 30 ASP cc_start: 0.8597 (t0) cc_final: 0.8308 (t0) REVERT: E 66 ASP cc_start: 0.9266 (t70) cc_final: 0.8645 (t0) REVERT: F 359 MET cc_start: 0.9120 (tmm) cc_final: 0.8787 (tmm) REVERT: F 458 ASP cc_start: 0.9054 (m-30) cc_final: 0.8685 (m-30) REVERT: J 16 TYR cc_start: 0.9274 (OUTLIER) cc_final: 0.8714 (p90) REVERT: J 19 ASP cc_start: 0.8353 (t70) cc_final: 0.7990 (t0) REVERT: J 84 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7929 (ppp) REVERT: M 41 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7893 (tm-30) REVERT: M 43 ASP cc_start: 0.8590 (t70) cc_final: 0.8239 (t0) REVERT: M 149 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8100 (ptmm) REVERT: Z 31 ASP cc_start: 0.8574 (p0) cc_final: 0.8306 (p0) outliers start: 123 outliers final: 83 residues processed: 247 average time/residue: 0.3469 time to fit residues: 149.3126 Evaluate side-chains 233 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 135 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 507 GLU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 149 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 0.9990 chunk 315 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 205 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 290 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN F 325 ASN ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30258 Z= 0.172 Angle : 0.547 10.773 41373 Z= 0.285 Chirality : 0.041 0.152 4713 Planarity : 0.004 0.066 5124 Dihedral : 17.013 171.370 4951 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 4.01 % Allowed : 19.02 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3546 helix: 1.33 (0.14), residues: 1389 sheet: -1.62 (0.26), residues: 398 loop : -1.57 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.003 0.000 HIS C 941 PHE 0.009 0.001 PHE C 153 TYR 0.014 0.001 TYR A 168 ARG 0.007 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 149 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.7551 (p90) REVERT: A 194 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9068 (tt) REVERT: B 39 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8639 (ttt-90) REVERT: B 188 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8641 (m-30) REVERT: C 127 MET cc_start: 0.8744 (pmm) cc_final: 0.8469 (pmm) REVERT: C 225 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7389 (ptm160) REVERT: C 263 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8687 (pp20) REVERT: C 402 GLU cc_start: 0.9555 (OUTLIER) cc_final: 0.9292 (pp20) REVERT: C 535 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8942 (mp0) REVERT: C 630 MET cc_start: 0.8771 (ttp) cc_final: 0.7877 (tmm) REVERT: C 1051 MET cc_start: 0.8993 (mmm) cc_final: 0.8601 (mmm) REVERT: C 1104 GLU cc_start: 0.8657 (pp20) cc_final: 0.8346 (pp20) REVERT: D 256 MET cc_start: 0.7225 (tmm) cc_final: 0.6011 (tmt) REVERT: D 310 MET cc_start: 0.8245 (mmm) cc_final: 0.7987 (mmm) REVERT: D 379 ASP cc_start: 0.8433 (m-30) cc_final: 0.7929 (m-30) REVERT: D 862 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8033 (p0) REVERT: D 953 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9154 (pp) REVERT: D 1025 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6984 (p) REVERT: D 1062 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: E 30 ASP cc_start: 0.8690 (t0) cc_final: 0.8477 (t0) REVERT: E 66 ASP cc_start: 0.9269 (t70) cc_final: 0.8635 (t0) REVERT: F 263 MET cc_start: 0.8674 (mmm) cc_final: 0.8314 (mpp) REVERT: F 359 MET cc_start: 0.9112 (tmm) cc_final: 0.8896 (ptp) REVERT: F 458 ASP cc_start: 0.9061 (m-30) cc_final: 0.8689 (m-30) REVERT: J 16 TYR cc_start: 0.9276 (OUTLIER) cc_final: 0.8688 (p90) REVERT: J 19 ASP cc_start: 0.8373 (t70) cc_final: 0.8005 (t0) REVERT: J 84 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7948 (ppp) REVERT: M 41 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7925 (tm-30) REVERT: M 43 ASP cc_start: 0.8558 (t70) cc_final: 0.8201 (t0) REVERT: M 149 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (ptmm) REVERT: Z 31 ASP cc_start: 0.8530 (p0) cc_final: 0.8271 (p0) outliers start: 119 outliers final: 79 residues processed: 255 average time/residue: 0.3588 time to fit residues: 156.2277 Evaluate side-chains 229 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 135 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 507 GLU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 294 optimal weight: 30.0000 chunk 195 optimal weight: 0.0020 chunk 348 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30258 Z= 0.229 Angle : 0.572 13.138 41373 Z= 0.296 Chirality : 0.042 0.208 4713 Planarity : 0.004 0.059 5124 Dihedral : 16.938 173.260 4944 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 4.07 % Allowed : 19.22 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3546 helix: 1.34 (0.14), residues: 1395 sheet: -1.62 (0.26), residues: 410 loop : -1.53 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 223 HIS 0.004 0.001 HIS F 516 PHE 0.018 0.001 PHE A 219 TYR 0.013 0.001 TYR A 168 ARG 0.005 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 137 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7507 (p90) REVERT: A 194 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9034 (tt) REVERT: B 39 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8686 (ttt-90) REVERT: B 188 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8652 (m-30) REVERT: C 225 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7319 (ptm160) REVERT: C 263 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8718 (pp20) REVERT: C 402 GLU cc_start: 0.9553 (OUTLIER) cc_final: 0.9295 (pp20) REVERT: C 535 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8955 (mp0) REVERT: C 593 MET cc_start: 0.8990 (mmm) cc_final: 0.8444 (mmm) REVERT: C 630 MET cc_start: 0.8804 (ttp) cc_final: 0.7632 (tmm) REVERT: C 1051 MET cc_start: 0.9016 (mmm) cc_final: 0.8654 (mmm) REVERT: C 1104 GLU cc_start: 0.8681 (pp20) cc_final: 0.8373 (pp20) REVERT: D 256 MET cc_start: 0.7337 (tmm) cc_final: 0.6113 (tmt) REVERT: D 310 MET cc_start: 0.8264 (mmm) cc_final: 0.7974 (mmm) REVERT: D 379 ASP cc_start: 0.8452 (m-30) cc_final: 0.7950 (m-30) REVERT: D 834 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8027 (tpm170) REVERT: D 862 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8141 (p0) REVERT: D 953 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9149 (pp) REVERT: D 991 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8570 (mm) REVERT: D 1025 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.7015 (p) REVERT: D 1062 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: D 1155 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8700 (mm-30) REVERT: E 30 ASP cc_start: 0.8660 (t0) cc_final: 0.8439 (t0) REVERT: E 66 ASP cc_start: 0.9271 (t70) cc_final: 0.8620 (t0) REVERT: F 359 MET cc_start: 0.9136 (tmm) cc_final: 0.8893 (tmm) REVERT: F 458 ASP cc_start: 0.9051 (m-30) cc_final: 0.8676 (m-30) REVERT: J 16 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8732 (p90) REVERT: J 19 ASP cc_start: 0.8290 (t70) cc_final: 0.7898 (t0) REVERT: J 84 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7949 (ppp) REVERT: M 41 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7802 (tm-30) REVERT: M 43 ASP cc_start: 0.8536 (t70) cc_final: 0.8196 (t0) REVERT: M 149 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8112 (ptmm) REVERT: Z 31 ASP cc_start: 0.8543 (p0) cc_final: 0.8274 (p0) outliers start: 121 outliers final: 89 residues processed: 245 average time/residue: 0.3604 time to fit residues: 149.8807 Evaluate side-chains 241 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 134 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain F residue 213 ARG Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain F residue 507 GLU Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 172 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30258 Z= 0.200 Angle : 0.555 11.342 41373 Z= 0.288 Chirality : 0.041 0.171 4713 Planarity : 0.004 0.059 5124 Dihedral : 16.885 176.668 4944 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 3.97 % Allowed : 19.52 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3546 helix: 1.40 (0.14), residues: 1403 sheet: -1.53 (0.26), residues: 405 loop : -1.47 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.003 0.001 HIS F 516 PHE 0.014 0.001 PHE A 219 TYR 0.013 0.001 TYR A 168 ARG 0.004 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 142 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7398 (p90) REVERT: B 39 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8747 (ttt-90) REVERT: B 188 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8659 (m-30) REVERT: C 225 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7259 (ptm160) REVERT: C 263 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8749 (pp20) REVERT: C 402 GLU cc_start: 0.9553 (OUTLIER) cc_final: 0.9286 (pp20) REVERT: C 535 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8960 (mp0) REVERT: C 593 MET cc_start: 0.9033 (mmm) cc_final: 0.8485 (mmm) REVERT: C 630 MET cc_start: 0.8827 (ttp) cc_final: 0.7661 (tmm) REVERT: C 1051 MET cc_start: 0.9042 (mmm) cc_final: 0.8672 (mmm) REVERT: C 1104 GLU cc_start: 0.8688 (pp20) cc_final: 0.8227 (pp20) REVERT: D 256 MET cc_start: 0.7410 (tmm) cc_final: 0.6170 (tmt) REVERT: D 379 ASP cc_start: 0.8393 (m-30) cc_final: 0.7872 (m-30) REVERT: D 674 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8591 (t0) REVERT: D 834 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8022 (tpm170) REVERT: D 862 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8018 (p0) REVERT: D 953 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9149 (pp) REVERT: D 991 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8571 (mm) REVERT: D 1155 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8655 (mm-30) REVERT: D 1208 MET cc_start: 0.8541 (ppp) cc_final: 0.7621 (ppp) REVERT: E 66 ASP cc_start: 0.9276 (t70) cc_final: 0.8621 (t0) REVERT: F 359 MET cc_start: 0.9128 (tmm) cc_final: 0.8908 (tmm) REVERT: F 458 ASP cc_start: 0.9044 (m-30) cc_final: 0.8670 (m-30) REVERT: J 16 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8684 (p90) REVERT: J 19 ASP cc_start: 0.8290 (t70) cc_final: 0.7890 (t0) REVERT: J 84 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7950 (ppp) REVERT: M 41 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7889 (tm-30) REVERT: M 43 ASP cc_start: 0.8513 (t70) cc_final: 0.8239 (t0) REVERT: Z 31 ASP cc_start: 0.8522 (p0) cc_final: 0.8283 (p0) outliers start: 118 outliers final: 84 residues processed: 245 average time/residue: 0.3807 time to fit residues: 160.6929 Evaluate side-chains 235 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 136 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 8.9990 chunk 334 optimal weight: 7.9990 chunk 304 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 195 optimal weight: 0.0870 chunk 141 optimal weight: 0.9990 chunk 255 optimal weight: 0.0040 chunk 99 optimal weight: 0.7980 chunk 293 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 324 optimal weight: 6.9990 overall best weight: 1.7774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30258 Z= 0.191 Angle : 0.568 12.781 41373 Z= 0.292 Chirality : 0.041 0.170 4713 Planarity : 0.004 0.059 5124 Dihedral : 16.836 177.835 4943 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 3.50 % Allowed : 20.13 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3546 helix: 1.44 (0.14), residues: 1404 sheet: -1.49 (0.26), residues: 400 loop : -1.43 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 938 HIS 0.002 0.001 HIS F 516 PHE 0.014 0.001 PHE C 153 TYR 0.013 0.001 TYR A 168 ARG 0.003 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 140 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7262 (p90) REVERT: B 39 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8756 (ttt-90) REVERT: B 188 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8662 (m-30) REVERT: C 225 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7469 (ptm160) REVERT: C 263 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8749 (pp20) REVERT: C 402 GLU cc_start: 0.9548 (OUTLIER) cc_final: 0.9276 (pp20) REVERT: C 535 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8962 (mp0) REVERT: C 593 MET cc_start: 0.9068 (mmm) cc_final: 0.8527 (mmm) REVERT: C 630 MET cc_start: 0.8823 (ttp) cc_final: 0.7730 (tmm) REVERT: C 1051 MET cc_start: 0.9045 (mmm) cc_final: 0.8676 (mmm) REVERT: C 1104 GLU cc_start: 0.8687 (pp20) cc_final: 0.8226 (pp20) REVERT: D 256 MET cc_start: 0.7402 (tmm) cc_final: 0.6149 (tmt) REVERT: D 379 ASP cc_start: 0.8387 (m-30) cc_final: 0.7861 (m-30) REVERT: D 674 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8583 (t0) REVERT: D 834 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8016 (tpm170) REVERT: D 862 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8005 (p0) REVERT: D 991 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8563 (mm) REVERT: D 1062 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: D 1155 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8657 (mm-30) REVERT: E 66 ASP cc_start: 0.9284 (t70) cc_final: 0.8622 (t0) REVERT: F 263 MET cc_start: 0.8184 (mmt) cc_final: 0.7885 (mmt) REVERT: F 458 ASP cc_start: 0.9036 (m-30) cc_final: 0.8663 (m-30) REVERT: J 16 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8702 (p90) REVERT: J 19 ASP cc_start: 0.8245 (t70) cc_final: 0.7845 (t0) REVERT: J 84 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7955 (ppp) REVERT: M 41 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8228 (tm-30) REVERT: M 43 ASP cc_start: 0.8517 (t70) cc_final: 0.8292 (t0) REVERT: Z 31 ASP cc_start: 0.8549 (p0) cc_final: 0.8246 (p0) outliers start: 104 outliers final: 81 residues processed: 229 average time/residue: 0.3672 time to fit residues: 142.3773 Evaluate side-chains 234 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 138 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain Z residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 1.9990 chunk 343 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 360 optimal weight: 8.9990 chunk 331 optimal weight: 7.9990 chunk 287 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30258 Z= 0.283 Angle : 0.603 11.122 41373 Z= 0.311 Chirality : 0.042 0.168 4713 Planarity : 0.004 0.059 5124 Dihedral : 16.858 178.518 4941 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 3.67 % Allowed : 19.96 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3546 helix: 1.36 (0.14), residues: 1407 sheet: -1.48 (0.26), residues: 402 loop : -1.44 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 223 HIS 0.011 0.001 HIS F 371 PHE 0.012 0.001 PHE A 219 TYR 0.013 0.001 TYR A 168 ARG 0.004 0.000 ARG D 875 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 132 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.7057 (p90) REVERT: B 39 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8759 (ttt-90) REVERT: B 188 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8635 (m-30) REVERT: C 225 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7504 (ptm160) REVERT: C 263 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8763 (pp20) REVERT: C 593 MET cc_start: 0.9044 (mmm) cc_final: 0.8449 (mmm) REVERT: C 630 MET cc_start: 0.8842 (ttp) cc_final: 0.7654 (tmm) REVERT: C 1051 MET cc_start: 0.9005 (mmm) cc_final: 0.8624 (mmm) REVERT: C 1104 GLU cc_start: 0.8710 (pp20) cc_final: 0.8254 (pp20) REVERT: D 256 MET cc_start: 0.7379 (tmm) cc_final: 0.6105 (tmt) REVERT: D 379 ASP cc_start: 0.8449 (m-30) cc_final: 0.7927 (m-30) REVERT: D 834 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8064 (tpm170) REVERT: D 862 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8153 (p0) REVERT: D 953 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9157 (pp) REVERT: D 1062 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: D 1155 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8722 (mm-30) REVERT: D 1208 MET cc_start: 0.8704 (ppp) cc_final: 0.7691 (ppp) REVERT: E 66 ASP cc_start: 0.9284 (t70) cc_final: 0.8660 (t0) REVERT: F 458 ASP cc_start: 0.9031 (m-30) cc_final: 0.8661 (m-30) REVERT: J 16 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8770 (p90) REVERT: J 19 ASP cc_start: 0.8248 (t70) cc_final: 0.7866 (t0) REVERT: J 84 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7961 (ppp) REVERT: M 43 ASP cc_start: 0.8540 (t70) cc_final: 0.8324 (t0) REVERT: Z 31 ASP cc_start: 0.8570 (p0) cc_final: 0.8327 (p0) outliers start: 109 outliers final: 88 residues processed: 227 average time/residue: 0.3600 time to fit residues: 139.5658 Evaluate side-chains 231 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 131 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 713 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 834 ARG Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1062 TYR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1155 GLU Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1264 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain Z residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5922 > 50: distance: 64 - 68: 4.302 distance: 68 - 69: 8.460 distance: 69 - 70: 3.520 distance: 69 - 72: 13.412 distance: 70 - 71: 31.885 distance: 70 - 76: 25.820 distance: 72 - 73: 25.933 distance: 73 - 74: 3.481 distance: 73 - 75: 9.043 distance: 76 - 77: 23.844 distance: 77 - 78: 10.454 distance: 77 - 80: 8.671 distance: 78 - 79: 9.026 distance: 78 - 82: 16.067 distance: 80 - 81: 29.561 distance: 82 - 83: 9.759 distance: 83 - 84: 12.410 distance: 83 - 86: 5.400 distance: 84 - 85: 10.564 distance: 84 - 90: 15.629 distance: 86 - 87: 8.335 distance: 86 - 88: 16.310 distance: 87 - 89: 9.322 distance: 90 - 91: 14.448 distance: 91 - 92: 10.787 distance: 91 - 94: 18.472 distance: 92 - 93: 11.883 distance: 92 - 96: 7.681 distance: 93 - 122: 20.592 distance: 94 - 95: 10.148 distance: 96 - 97: 12.973 distance: 96 - 102: 20.641 distance: 97 - 98: 14.941 distance: 97 - 100: 15.516 distance: 98 - 99: 7.245 distance: 98 - 103: 9.246 distance: 99 - 127: 7.843 distance: 100 - 101: 11.685 distance: 101 - 102: 8.397 distance: 103 - 104: 15.460 distance: 104 - 105: 13.012 distance: 105 - 106: 12.220 distance: 105 - 114: 5.826 distance: 106 - 135: 12.420 distance: 107 - 108: 10.423 distance: 108 - 109: 16.124 distance: 109 - 110: 12.700 distance: 110 - 111: 12.928 distance: 111 - 112: 17.207 distance: 111 - 113: 18.970 distance: 114 - 115: 13.053 distance: 115 - 116: 7.162 distance: 115 - 118: 7.206 distance: 116 - 117: 3.089 distance: 116 - 122: 8.166 distance: 117 - 140: 10.025 distance: 118 - 119: 7.309 distance: 119 - 120: 9.929 distance: 119 - 121: 4.070 distance: 122 - 123: 6.272 distance: 123 - 124: 5.221 distance: 123 - 126: 5.775 distance: 124 - 125: 3.168 distance: 124 - 127: 4.991 distance: 125 - 146: 5.620 distance: 128 - 131: 6.055 distance: 130 - 151: 9.637 distance: 131 - 132: 3.403 distance: 132 - 133: 7.655 distance: 132 - 134: 4.937 distance: 136 - 137: 5.018 distance: 136 - 139: 3.453 distance: 137 - 138: 9.325 distance: 137 - 140: 15.518 distance: 138 - 155: 23.304