Starting phenix.real_space_refine on Thu Mar 21 08:05:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/03_2024/7kim_22887_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/03_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_22887/03_2024/7kim_22887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/03_2024/7kim_22887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/03_2024/7kim_22887_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kim_22887/03_2024/7kim_22887_updated.pdb" } 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-5265/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: 15.79, per 1000 atoms: 0.53 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: 12.35 Conformation dependent library (CDL) restraints added in 5.4 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... running ksdssp... Secondary structure from input PDB file: 115 helices and 30 sheets defined 35.8% alpha, 7.6% beta 44 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 13.30 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 73 through 82 removed outlier: 4.581A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 204 through 223 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 31 through 44 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 73 through 80 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.870A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 65 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 289 through 300 removed outlier: 3.642A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 319 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 381 through 406 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 414 through 417 No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 421 through 431 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 590 through 592 No H-bonds generated for 'chain 'C' and resid 590 through 592' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 602 through 613 removed outlier: 4.396A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 740 through 743 No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 929 through 942 Processing helix chain 'C' and resid 954 through 957 removed outlier: 3.675A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 954 through 957' Processing helix chain 'C' and resid 982 through 990 Processing helix chain 'C' and resid 1070 through 1079 Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1096 through 1108 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 1119 through 1130 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.524A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 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 142 through 185 removed outlier: 4.063A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 227 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 238 through 248 Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 287 through 304 removed outlier: 4.548A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 360 Processing helix chain 'D' and resid 364 through 382 Processing helix chain 'D' and resid 394 through 396 No H-bonds generated for 'chain 'D' and resid 394 through 396' Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 408 through 410 No H-bonds generated for 'chain 'D' and resid 408 through 410' Processing helix chain 'D' and resid 445 through 451 removed outlier: 4.114A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 462 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 481 through 491 removed outlier: 3.728A pdb=" N TRP D 484 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU D 488 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 508 No H-bonds generated for 'chain 'D' and resid 506 through 508' Processing helix chain 'D' and resid 529 through 532 No H-bonds generated for 'chain 'D' and resid 529 through 532' Processing helix chain 'D' and resid 549 through 557 Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 615 through 623 Processing helix chain 'D' and resid 644 through 650 Processing helix chain 'D' and resid 669 through 674 Processing helix chain 'D' and resid 690 through 703 Processing helix chain 'D' and resid 706 through 724 Processing helix chain 'D' and resid 742 through 761 removed outlier: 3.832A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 792 Processing helix chain 'D' and resid 798 through 804 Processing helix chain 'D' and resid 811 through 817 Processing helix chain 'D' and resid 846 through 880 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 946 through 955 Processing helix chain 'D' and resid 976 through 979 No H-bonds generated for 'chain 'D' and resid 976 through 979' Processing helix chain 'D' and resid 995 through 1005 Processing helix chain 'D' and resid 1028 through 1036 Processing helix chain 'D' and resid 1118 through 1145 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) removed outlier: 4.008A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1161 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) Processing helix chain 'D' and resid 1183 through 1192 Processing helix chain 'D' and resid 1210 through 1215 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 4.185A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1239 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 1249 through 1253 removed outlier: 3.723A pdb=" N ILE D1253 " --> pdb=" O LYS D1249 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1249 through 1253' Processing helix chain 'D' and resid 1276 through 1279 No H-bonds generated for 'chain 'D' and resid 1276 through 1279' Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 40 through 45 removed outlier: 4.568A pdb=" N ASP E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 69 Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'F' and resid 209 through 222 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) Processing helix chain 'F' and resid 228 through 237 removed outlier: 4.047A pdb=" N LYS F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 267 Processing helix chain 'F' and resid 275 through 310 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) removed outlier: 4.820A pdb=" N ARG F 309 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 333 Processing helix chain 'F' and resid 343 through 361 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 370 through 390 Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 417 Processing helix chain 'F' and resid 435 through 438 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 479 Processing helix chain 'F' and resid 489 through 496 Processing helix chain 'F' and resid 500 through 515 Processing helix chain 'F' and resid 517 through 520 No H-bonds generated for 'chain 'F' and resid 517 through 520' Processing helix chain 'J' and resid 81 through 86 Processing helix chain 'J' and resid 91 through 109 Processing helix chain 'M' and resid 50 through 56 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 64 through 75 Processing helix chain 'M' and resid 88 through 98 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 101 through 104 No H-bonds generated for 'chain 'M' and resid 101 through 104' Processing helix chain 'M' and resid 126 through 142 Processing helix chain 'M' and resid 149 through 159 removed outlier: 3.971A pdb=" N ALA M 159 " --> pdb=" O GLU M 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 29 Processing helix chain 'Z' and resid 37 through 45 removed outlier: 3.592A pdb=" N CYS Z 43 " --> pdb=" O ALA Z 39 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL Z 44 " --> pdb=" O LYS Z 40 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 59 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 15 removed outlier: 6.916A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 54 through 56 removed outlier: 3.568A pdb=" N VAL A 136 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 93 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= D, 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= E, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.952A pdb=" N SER B 53 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 171 through 177 removed outlier: 7.018A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 104 through 108 Processing sheet with id= H, first strand: chain 'C' and resid 166 through 168 Processing sheet with id= I, first strand: chain 'C' and resid 178 through 181 Processing sheet with id= J, first strand: chain 'C' and resid 185 through 187 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= K, first strand: chain 'C' and resid 354 through 356 Processing sheet with id= L, first strand: chain 'C' and resid 514 through 516 Processing sheet with id= M, 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= N, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.645A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 716 through 722 removed outlier: 3.508A pdb=" N GLY C1026 " --> pdb=" O VAL C 721 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 748 through 750 Processing sheet with id= Q, 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) Processing sheet with id= R, first strand: chain 'C' and resid 884 through 886 Processing sheet with id= S, first strand: chain 'C' and resid 130 through 135 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= T, 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: 6.695A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 426 through 429 removed outlier: 3.643A pdb=" N HIS D 544 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 430 through 432 removed outlier: 6.140A pdb=" N ILE D 522 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 635 through 637 Processing sheet with id= X, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.827A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 1064 through 1066 Processing sheet with id= Z, 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= AA, first strand: chain 'J' and resid 29 through 33 Processing sheet with id= AB, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= AC, first strand: chain 'M' and resid 8 through 11 Processing sheet with id= AD, first strand: chain 'M' and resid 34 through 37 919 hydrogen bonds defined for protein. 2634 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: 11.65 Time building geometry restraints manager: 13.32 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: 10539 2.85 - 3.53: 42315 3.53 - 4.22: 68410 4.22 - 4.90: 114156 Nonbonded interactions: 235427 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 235422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.290 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 95.300 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.120 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.510 ------------------------------------------------------------------------------- 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= 0.544 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 : 3.363 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: 0.3439 time to fit residues: 208.7843 Evaluate side-chains 243 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 129 time to evaluate : 3.125 ------------------------------------------------------------------------------- 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: 0.1980 chunk 152 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 185 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 283 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 328 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN D 674 ASN D 854 HIS ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 30258 Z= 0.152 Angle : 0.550 11.905 41373 Z= 0.292 Chirality : 0.041 0.180 4713 Planarity : 0.005 0.067 5124 Dihedral : 17.711 161.926 5073 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 4.17 % Allowed : 17.87 % Favored : 77.95 % 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: 0.33 (0.14), residues: 1374 sheet: -2.04 (0.25), residues: 411 loop : -1.93 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 223 HIS 0.003 0.001 HIS C 941 PHE 0.009 0.001 PHE D1186 TYR 0.017 0.001 TYR A 168 ARG 0.003 0.000 ARG D 636 *********************** 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 277 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 153 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.7203 (p90) REVERT: B 117 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.9033 (p) REVERT: C 127 MET cc_start: 0.8982 (pmm) cc_final: 0.8491 (pmm) REVERT: C 611 MET cc_start: 0.8289 (ptp) cc_final: 0.7881 (ptp) REVERT: C 630 MET cc_start: 0.8647 (ttp) cc_final: 0.8249 (tmm) REVERT: C 656 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8537 (p0) REVERT: C 661 MET cc_start: 0.8396 (tpp) cc_final: 0.8043 (tpp) REVERT: C 723 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9052 (mm) REVERT: C 730 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8981 (p0) REVERT: C 1035 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7110 (m-70) REVERT: C 1051 MET cc_start: 0.8963 (mmm) cc_final: 0.8622 (mmm) REVERT: C 1076 MET cc_start: 0.9297 (mmm) cc_final: 0.9059 (mmm) REVERT: C 1104 GLU cc_start: 0.8579 (pp20) cc_final: 0.8300 (pp20) REVERT: D 92 MET cc_start: 0.8805 (mmt) cc_final: 0.8417 (mmm) REVERT: D 379 ASP cc_start: 0.8401 (m-30) cc_final: 0.7932 (m-30) REVERT: D 862 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8108 (p0) REVERT: D 953 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9057 (mm) REVERT: D 991 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8680 (mm) REVERT: E 35 ILE cc_start: 0.9561 (tt) cc_final: 0.9320 (tt) REVERT: E 66 ASP cc_start: 0.9241 (t70) cc_final: 0.8643 (t0) REVERT: E 102 ASP cc_start: 0.9328 (t0) cc_final: 0.9047 (t0) REVERT: F 357 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8928 (ttp80) REVERT: F 359 MET cc_start: 0.9132 (tmm) cc_final: 0.8783 (tmm) REVERT: F 458 ASP cc_start: 0.9062 (m-30) cc_final: 0.8694 (m-30) REVERT: J 16 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.8781 (p90) REVERT: J 19 ASP cc_start: 0.8311 (t70) cc_final: 0.7952 (t0) REVERT: J 84 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7905 (ppp) REVERT: M 41 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7924 (tm-30) REVERT: M 43 ASP cc_start: 0.8310 (t70) cc_final: 0.7996 (t0) outliers start: 124 outliers final: 67 residues processed: 267 average time/residue: 0.3525 time to fit residues: 164.1946 Evaluate side-chains 212 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 133 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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 198 THR 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 84 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 195 THR 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 380 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 730 ASN Chi-restraints excluded: chain C residue 758 ASP 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 C residue 1035 HIS 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 139 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 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 425 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 667 THR 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 825 THR 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 985 THR Chi-restraints excluded: chain D residue 991 ILE 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 213 ARG Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 357 ARG 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 7 ASP 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 101 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: 0.9990 chunk 102 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 329 optimal weight: 20.0000 chunk 355 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 264 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN D 674 ASN D 687 GLN F 325 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 30258 Z= 0.360 Angle : 0.624 11.710 41373 Z= 0.327 Chirality : 0.042 0.216 4713 Planarity : 0.004 0.067 5124 Dihedral : 17.466 161.390 4985 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.41 % Rotamer: Outliers : 5.08 % Allowed : 18.31 % Favored : 76.61 % 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: -1.14 (0.14), residues: 3546 helix: 0.84 (0.14), residues: 1364 sheet: -1.99 (0.25), residues: 435 loop : -1.75 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 223 HIS 0.007 0.001 HIS F 516 PHE 0.010 0.001 PHE C 61 TYR 0.017 0.001 TYR A 168 ARG 0.003 0.000 ARG Z 85 *********************** 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 281 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 130 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7658 (p90) REVERT: B 39 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8651 (ttt-90) REVERT: B 117 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9050 (p) REVERT: B 188 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8644 (m-30) REVERT: C 124 ASP cc_start: 0.9294 (OUTLIER) cc_final: 0.9072 (p0) REVERT: C 127 MET cc_start: 0.8918 (pmm) cc_final: 0.8693 (pmm) REVERT: C 225 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7482 (ptm160) REVERT: C 611 MET cc_start: 0.8344 (ptp) cc_final: 0.7947 (ptp) REVERT: C 630 MET cc_start: 0.8890 (ttp) cc_final: 0.8268 (tmm) REVERT: C 661 MET cc_start: 0.8273 (tpp) cc_final: 0.7992 (tpp) REVERT: C 723 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9267 (mm) REVERT: C 1035 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7111 (m-70) REVERT: C 1104 GLU cc_start: 0.8655 (pp20) cc_final: 0.8392 (pp20) REVERT: D 256 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6342 (tmm) REVERT: D 379 ASP cc_start: 0.8517 (m-30) cc_final: 0.8089 (m-30) REVERT: D 541 MET cc_start: 0.8420 (mtp) cc_final: 0.8177 (mtp) REVERT: D 862 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8175 (p0) REVERT: D 879 ASP cc_start: 0.8400 (m-30) cc_final: 0.8182 (m-30) REVERT: D 953 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9175 (pp) REVERT: E 66 ASP cc_start: 0.9276 (t70) cc_final: 0.8685 (t0) REVERT: E 102 ASP cc_start: 0.9351 (t0) cc_final: 0.9111 (t0) REVERT: F 359 MET cc_start: 0.9094 (tmm) cc_final: 0.8722 (tmm) REVERT: F 458 ASP cc_start: 0.9086 (m-30) cc_final: 0.8725 (m-30) REVERT: J 16 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8782 (p90) REVERT: J 19 ASP cc_start: 0.8423 (t70) cc_final: 0.8092 (t0) REVERT: J 84 MET cc_start: 0.8234 (ppp) cc_final: 0.7853 (ppp) REVERT: M 41 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7830 (tm-30) REVERT: M 43 ASP cc_start: 0.8437 (t70) cc_final: 0.8080 (t0) REVERT: Z 31 ASP cc_start: 0.8681 (p0) cc_final: 0.8374 (p0) outliers start: 151 outliers final: 100 residues processed: 268 average time/residue: 0.3461 time to fit residues: 161.2866 Evaluate side-chains 238 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 126 time to evaluate : 3.254 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 226 ASN 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 56 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL 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 B residue 227 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 171 THR 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 380 THR Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 532 THR 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 656 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 758 ASP 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 880 SER Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 907 LEU 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 1035 HIS Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 425 SER 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 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 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 825 THR 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 1053 VAL 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 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 446 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 98 LEU Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain Z residue 27 LEU 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: 0.0570 chunk 247 optimal weight: 6.9990 chunk 170 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 221 optimal weight: 0.9980 chunk 330 optimal weight: 7.9990 chunk 349 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 313 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 4.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30258 Z= 0.336 Angle : 0.599 8.766 41373 Z= 0.315 Chirality : 0.042 0.195 4713 Planarity : 0.004 0.062 5124 Dihedral : 17.403 163.098 4977 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.67 % Favored : 92.24 % Rotamer: Outliers : 5.45 % Allowed : 18.95 % Favored : 75.60 % 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: -1.01 (0.14), residues: 3546 helix: 0.96 (0.14), residues: 1372 sheet: -1.93 (0.25), residues: 427 loop : -1.70 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 223 HIS 0.006 0.001 HIS F 516 PHE 0.010 0.001 PHE C 61 TYR 0.016 0.001 TYR A 168 ARG 0.012 0.000 ARG F 357 *********************** 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 297 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 135 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.7665 (p90) REVERT: B 39 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8610 (ttt-90) REVERT: B 117 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9087 (p) REVERT: C 124 ASP cc_start: 0.9296 (OUTLIER) cc_final: 0.9081 (p0) REVERT: C 127 MET cc_start: 0.8754 (pmm) cc_final: 0.8480 (pmm) REVERT: C 225 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7410 (ptm160) REVERT: C 611 MET cc_start: 0.8346 (ptp) cc_final: 0.7885 (ptp) REVERT: C 630 MET cc_start: 0.8916 (ttp) cc_final: 0.8239 (tmm) REVERT: C 661 MET cc_start: 0.8240 (tpp) cc_final: 0.7970 (tpp) REVERT: C 723 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9214 (mm) REVERT: C 724 MET cc_start: 0.8726 (ptm) cc_final: 0.8412 (ppp) REVERT: C 1035 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7083 (m-70) REVERT: C 1051 MET cc_start: 0.8987 (mmm) cc_final: 0.8526 (mmm) REVERT: C 1104 GLU cc_start: 0.8658 (pp20) cc_final: 0.8399 (pp20) REVERT: D 92 MET cc_start: 0.8834 (mmt) cc_final: 0.8512 (mmm) REVERT: D 256 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6264 (tmm) REVERT: D 379 ASP cc_start: 0.8524 (m-30) cc_final: 0.8103 (m-30) REVERT: D 541 MET cc_start: 0.8431 (mtp) cc_final: 0.8159 (mtp) REVERT: D 862 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8226 (p0) REVERT: D 879 ASP cc_start: 0.8419 (m-30) cc_final: 0.8186 (m-30) REVERT: D 953 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9173 (pp) REVERT: D 1025 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6792 (p) REVERT: E 66 ASP cc_start: 0.9272 (t70) cc_final: 0.8649 (t0) REVERT: E 102 ASP cc_start: 0.9356 (t0) cc_final: 0.9147 (t0) REVERT: F 359 MET cc_start: 0.9148 (tmm) cc_final: 0.8775 (tmm) REVERT: F 458 ASP cc_start: 0.9060 (m-30) cc_final: 0.8701 (m-30) REVERT: F 507 GLU cc_start: 0.9493 (OUTLIER) cc_final: 0.9274 (pp20) REVERT: J 16 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.8808 (p90) REVERT: J 19 ASP cc_start: 0.8347 (t70) cc_final: 0.8007 (t0) REVERT: J 84 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7907 (ppp) REVERT: M 41 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7835 (tm-30) REVERT: M 43 ASP cc_start: 0.8518 (t70) cc_final: 0.8132 (t0) REVERT: Z 31 ASP cc_start: 0.8707 (p0) cc_final: 0.8390 (p0) outliers start: 162 outliers final: 105 residues processed: 282 average time/residue: 0.3340 time to fit residues: 165.6062 Evaluate side-chains 250 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 131 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 22 VAL 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 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 226 ASN 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 56 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 196 ASP 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 380 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 626 VAL 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 690 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 758 ASP 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 839 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 881 ASP 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 1035 HIS Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1102 VAL 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 139 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU 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 782 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 825 THR 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 1014 THR Chi-restraints excluded: chain D residue 1025 THR 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 F residue 213 ARG Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 366 ILE 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 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 7 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 27 LEU 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: 50.0000 chunk 198 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 260 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 30258 Z= 0.293 Angle : 0.576 9.826 41373 Z= 0.302 Chirality : 0.041 0.173 4713 Planarity : 0.004 0.060 5124 Dihedral : 17.256 165.333 4973 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.39 % Rotamer: Outliers : 5.42 % Allowed : 19.59 % Favored : 74.99 % 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: -0.85 (0.14), residues: 3546 helix: 1.11 (0.14), residues: 1372 sheet: -1.88 (0.25), residues: 420 loop : -1.63 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 223 HIS 0.005 0.001 HIS F 516 PHE 0.008 0.001 PHE C 61 TYR 0.016 0.001 TYR A 168 ARG 0.004 0.000 ARG Z 49 *********************** 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 295 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 134 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: A 168 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.7582 (p90) REVERT: B 39 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8604 (ttt-90) REVERT: B 117 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9103 (p) REVERT: C 127 MET cc_start: 0.8777 (pmm) cc_final: 0.8490 (pmm) REVERT: C 225 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7457 (ptm160) REVERT: C 402 GLU cc_start: 0.9568 (OUTLIER) cc_final: 0.9323 (pp20) REVERT: C 611 MET cc_start: 0.8281 (ptp) cc_final: 0.7849 (ptp) REVERT: C 630 MET cc_start: 0.8878 (ttp) cc_final: 0.8238 (tmm) REVERT: C 661 MET cc_start: 0.8215 (tpp) cc_final: 0.7947 (tpp) REVERT: C 723 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9271 (mm) REVERT: C 724 MET cc_start: 0.8716 (ptm) cc_final: 0.8386 (ptt) REVERT: C 839 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8986 (m) REVERT: C 1035 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7019 (m-70) REVERT: C 1051 MET cc_start: 0.8949 (mmm) cc_final: 0.8534 (mmm) REVERT: C 1104 GLU cc_start: 0.8680 (pp20) cc_final: 0.8382 (pp20) REVERT: D 92 MET cc_start: 0.8865 (mmt) cc_final: 0.8468 (mmm) REVERT: D 256 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6239 (tmm) REVERT: D 285 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8566 (ttpp) REVERT: D 379 ASP cc_start: 0.8537 (m-30) cc_final: 0.8127 (m-30) REVERT: D 834 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8107 (tpm170) REVERT: D 862 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8257 (p0) REVERT: D 879 ASP cc_start: 0.8395 (m-30) cc_final: 0.8158 (m-30) REVERT: D 953 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9177 (pp) REVERT: D 1025 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6845 (p) REVERT: E 66 ASP cc_start: 0.9282 (t70) cc_final: 0.8650 (t0) REVERT: E 102 ASP cc_start: 0.9347 (t0) cc_final: 0.9141 (t0) REVERT: F 359 MET cc_start: 0.9147 (tmm) cc_final: 0.8907 (tmm) REVERT: F 458 ASP cc_start: 0.9052 (m-30) cc_final: 0.8692 (m-30) REVERT: J 16 TYR cc_start: 0.9369 (OUTLIER) cc_final: 0.8879 (p90) REVERT: J 19 ASP cc_start: 0.8219 (t70) cc_final: 0.7855 (t0) REVERT: J 84 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7897 (ppp) REVERT: M 41 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7905 (tm-30) REVERT: M 43 ASP cc_start: 0.8466 (t70) cc_final: 0.8124 (t0) REVERT: Z 31 ASP cc_start: 0.8731 (p0) cc_final: 0.8393 (p0) outliers start: 161 outliers final: 117 residues processed: 279 average time/residue: 0.3455 time to fit residues: 167.0677 Evaluate side-chains 266 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 132 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 22 VAL 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 175 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 226 ASN 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 56 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 175 THR 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 120 ASP Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 196 ASP 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 380 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 589 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 654 SER Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 790 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 880 SER Chi-restraints excluded: chain C residue 881 ASP 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 1035 HIS Chi-restraints excluded: chain C residue 1045 SER 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 48 CYS Chi-restraints excluded: chain D residue 60 CYS 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 160 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 342 ASP 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 515 MET Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 638 THR 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 725 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 825 THR 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 944 LEU Chi-restraints excluded: chain D residue 953 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1173 THR 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 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 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 24 LEU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 77 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 5.9990 chunk 315 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 350 optimal weight: 20.0000 chunk 290 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 0.0670 chunk 183 optimal weight: 0.0060 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN D 687 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30258 Z= 0.132 Angle : 0.514 10.553 41373 Z= 0.268 Chirality : 0.040 0.138 4713 Planarity : 0.004 0.061 5124 Dihedral : 16.981 170.202 4971 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 4.01 % Allowed : 21.14 % Favored : 74.86 % 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: -0.51 (0.15), residues: 3546 helix: 1.49 (0.14), residues: 1357 sheet: -1.58 (0.26), residues: 403 loop : -1.53 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 28 HIS 0.003 0.000 HIS C 941 PHE 0.010 0.001 PHE C 254 TYR 0.014 0.001 TYR A 168 ARG 0.005 0.000 ARG C 259 *********************** 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 275 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 156 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.7595 (p90) REVERT: B 39 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8535 (ttt-90) REVERT: C 127 MET cc_start: 0.8858 (pmm) cc_final: 0.8585 (pmm) REVERT: C 263 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8717 (pp20) REVERT: C 402 GLU cc_start: 0.9557 (OUTLIER) cc_final: 0.9304 (pp20) REVERT: C 630 MET cc_start: 0.8717 (ttp) cc_final: 0.8039 (tmm) REVERT: C 723 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9063 (mm) REVERT: C 1035 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7035 (m-70) REVERT: C 1051 MET cc_start: 0.9004 (mmm) cc_final: 0.8623 (mmm) REVERT: C 1104 GLU cc_start: 0.8616 (pp20) cc_final: 0.8288 (pp20) REVERT: D 92 MET cc_start: 0.8835 (mmt) cc_final: 0.8593 (mmm) REVERT: D 256 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.6361 (tmm) REVERT: D 327 MET cc_start: 0.8600 (tpt) cc_final: 0.8384 (tpt) REVERT: D 379 ASP cc_start: 0.8384 (m-30) cc_final: 0.7886 (m-30) REVERT: D 862 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8132 (p0) REVERT: D 879 ASP cc_start: 0.8208 (m-30) cc_final: 0.7919 (m-30) REVERT: D 953 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9181 (pp) REVERT: D 1025 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.7032 (p) REVERT: E 66 ASP cc_start: 0.9260 (t70) cc_final: 0.8588 (t0) REVERT: E 102 ASP cc_start: 0.9318 (t0) cc_final: 0.9099 (t0) REVERT: F 458 ASP cc_start: 0.9047 (m-30) cc_final: 0.8674 (m-30) REVERT: J 16 TYR cc_start: 0.9341 (OUTLIER) cc_final: 0.8910 (p90) REVERT: J 19 ASP cc_start: 0.8233 (t70) cc_final: 0.7868 (t0) REVERT: J 84 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8046 (ppp) REVERT: M 41 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7944 (tm-30) REVERT: M 43 ASP cc_start: 0.8652 (t70) cc_final: 0.8344 (t0) REVERT: Z 31 ASP cc_start: 0.8697 (p0) cc_final: 0.8347 (p0) outliers start: 119 outliers final: 77 residues processed: 259 average time/residue: 0.3579 time to fit residues: 158.3347 Evaluate side-chains 232 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 143 time to evaluate : 3.087 ------------------------------------------------------------------------------- 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 A residue 226 ASN 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 41 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 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 120 ASP Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 656 ASP 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 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 60 CYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 515 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 725 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR 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 974 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1173 THR 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 315 MET 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 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 294 optimal weight: 40.0000 chunk 195 optimal weight: 6.9990 chunk 348 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 HIS ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 30258 Z= 0.389 Angle : 0.630 8.861 41373 Z= 0.327 Chirality : 0.042 0.204 4713 Planarity : 0.005 0.074 5124 Dihedral : 17.042 171.077 4960 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.76 % Favored : 92.16 % Rotamer: Outliers : 4.68 % Allowed : 21.44 % Favored : 73.88 % 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: -0.71 (0.15), residues: 3546 helix: 1.27 (0.14), residues: 1374 sheet: -1.74 (0.25), residues: 420 loop : -1.60 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 66 HIS 0.007 0.001 HIS F 516 PHE 0.021 0.001 PHE A 219 TYR 0.014 0.001 TYR A 168 ARG 0.009 0.000 ARG C 259 *********************** 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 274 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 135 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.7148 (p90) REVERT: B 39 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8626 (ttt-90) REVERT: C 124 ASP cc_start: 0.9297 (OUTLIER) cc_final: 0.9086 (p0) REVERT: C 127 MET cc_start: 0.8775 (pmm) cc_final: 0.8410 (pmm) REVERT: C 225 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7288 (ptm160) REVERT: C 593 MET cc_start: 0.9079 (mmm) cc_final: 0.8571 (mmm) REVERT: C 630 MET cc_start: 0.8883 (ttp) cc_final: 0.7688 (tmm) REVERT: C 661 MET cc_start: 0.8361 (tpp) cc_final: 0.8124 (tpp) REVERT: C 1035 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6882 (m-70) REVERT: C 1104 GLU cc_start: 0.8707 (pp20) cc_final: 0.8429 (pp20) REVERT: D 92 MET cc_start: 0.8825 (mmt) cc_final: 0.8433 (mmm) REVERT: D 256 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.6370 (tmm) REVERT: D 379 ASP cc_start: 0.8560 (m-30) cc_final: 0.8151 (m-30) REVERT: D 450 GLU cc_start: 0.8463 (tp30) cc_final: 0.8256 (tp30) REVERT: D 834 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8087 (tpm170) REVERT: D 862 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8210 (p0) REVERT: D 879 ASP cc_start: 0.8318 (m-30) cc_final: 0.8069 (m-30) REVERT: D 953 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9181 (mm) REVERT: D 1025 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6939 (p) REVERT: E 66 ASP cc_start: 0.9294 (t70) cc_final: 0.8676 (t0) REVERT: F 268 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6670 (pp20) REVERT: F 359 MET cc_start: 0.9174 (tmm) cc_final: 0.8947 (tmm) REVERT: F 458 ASP cc_start: 0.9086 (m-30) cc_final: 0.8734 (m-30) REVERT: J 16 TYR cc_start: 0.9405 (OUTLIER) cc_final: 0.8957 (p90) REVERT: J 19 ASP cc_start: 0.8227 (t70) cc_final: 0.7874 (t0) REVERT: J 84 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8040 (ppp) REVERT: M 41 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7794 (tm-30) REVERT: M 43 ASP cc_start: 0.8566 (t70) cc_final: 0.8251 (t0) REVERT: Z 31 ASP cc_start: 0.8675 (p0) cc_final: 0.8363 (p0) outliers start: 139 outliers final: 111 residues processed: 259 average time/residue: 0.3435 time to fit residues: 154.6701 Evaluate side-chains 257 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 133 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 SER 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 175 THR 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 41 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 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 86 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 196 ASP 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 370 ILE Chi-restraints excluded: chain C residue 458 LEU 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 534 ASP Chi-restraints excluded: chain C residue 579 MET 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 654 SER Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 796 VAL 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 881 ASP 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 1035 HIS Chi-restraints excluded: chain C residue 1053 THR Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain D residue 517 VAL 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 725 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR 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 878 VAL 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 974 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1225 SER Chi-restraints excluded: chain D residue 1230 THR 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 268 GLU 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 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 7 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 chunk 32 optimal weight: 0.0670 chunk 274 optimal weight: 0.2980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30258 Z= 0.139 Angle : 0.526 10.835 41373 Z= 0.273 Chirality : 0.040 0.158 4713 Planarity : 0.004 0.060 5124 Dihedral : 16.920 176.146 4960 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.50 % Allowed : 22.65 % Favored : 73.85 % 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: -0.38 (0.15), residues: 3546 helix: 1.59 (0.14), residues: 1361 sheet: -1.39 (0.27), residues: 403 loop : -1.49 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 28 HIS 0.003 0.000 HIS C 941 PHE 0.010 0.001 PHE A 219 TYR 0.014 0.001 TYR A 168 ARG 0.010 0.000 ARG D 500 *********************** 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 248 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 144 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.7237 (p90) REVERT: B 39 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8559 (ttt-90) REVERT: B 173 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8861 (ttmm) REVERT: C 127 MET cc_start: 0.8865 (pmm) cc_final: 0.8522 (pmm) REVERT: C 263 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8666 (pp20) REVERT: C 593 MET cc_start: 0.9069 (mmm) cc_final: 0.8613 (mmm) REVERT: C 630 MET cc_start: 0.8738 (ttp) cc_final: 0.7924 (tmm) REVERT: C 661 MET cc_start: 0.8294 (tpp) cc_final: 0.8032 (tpp) REVERT: C 723 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9068 (mm) REVERT: C 1035 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7055 (m-70) REVERT: C 1051 MET cc_start: 0.8983 (mmm) cc_final: 0.7863 (mmm) REVERT: C 1104 GLU cc_start: 0.8621 (pp20) cc_final: 0.8291 (pp20) REVERT: D 92 MET cc_start: 0.8816 (mmt) cc_final: 0.8577 (mmm) REVERT: D 256 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.6357 (tmm) REVERT: D 379 ASP cc_start: 0.8419 (m-30) cc_final: 0.7941 (m-30) REVERT: D 862 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8101 (p0) REVERT: D 879 ASP cc_start: 0.8192 (m-30) cc_final: 0.7961 (m-30) REVERT: E 35 ILE cc_start: 0.9540 (tt) cc_final: 0.9306 (tt) REVERT: E 66 ASP cc_start: 0.9263 (t70) cc_final: 0.8569 (t0) REVERT: F 263 MET cc_start: 0.8693 (mmm) cc_final: 0.8282 (mpp) REVERT: F 359 MET cc_start: 0.9145 (tmm) cc_final: 0.8856 (tmm) REVERT: F 458 ASP cc_start: 0.9048 (m-30) cc_final: 0.8686 (m-30) REVERT: J 16 TYR cc_start: 0.9370 (OUTLIER) cc_final: 0.9007 (p90) REVERT: J 19 ASP cc_start: 0.8273 (t70) cc_final: 0.7916 (t0) REVERT: J 84 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8101 (ppp) REVERT: M 41 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8223 (tm-30) REVERT: M 43 ASP cc_start: 0.8588 (t70) cc_final: 0.8344 (t0) outliers start: 104 outliers final: 81 residues processed: 235 average time/residue: 0.3564 time to fit residues: 143.9570 Evaluate side-chains 230 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 140 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL 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 41 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 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 C residue 83 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 690 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 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 1035 HIS Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 515 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 713 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR 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 974 VAL 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 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 395 THR Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain F residue 488 THR Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain Z residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 62.538 > 50: distance: 52 - 68: 16.558 distance: 57 - 76: 30.827 distance: 64 - 68: 14.143 distance: 68 - 69: 10.135 distance: 69 - 70: 10.532 distance: 69 - 72: 6.297 distance: 70 - 71: 26.065 distance: 72 - 73: 35.400 distance: 73 - 75: 38.590 distance: 76 - 77: 7.349 distance: 77 - 78: 11.873 distance: 77 - 80: 18.710 distance: 78 - 79: 30.376 distance: 78 - 82: 14.332 distance: 80 - 81: 9.309 distance: 82 - 83: 14.322 distance: 83 - 84: 27.978 distance: 83 - 86: 4.939 distance: 84 - 88: 12.135 distance: 86 - 87: 18.127 distance: 88 - 89: 4.037 distance: 89 - 90: 21.150 distance: 89 - 92: 26.456 distance: 90 - 91: 21.609 distance: 90 - 95: 16.995 distance: 92 - 93: 3.496 distance: 92 - 94: 3.123 distance: 95 - 96: 8.961 distance: 96 - 97: 11.080 distance: 96 - 99: 4.139 distance: 97 - 98: 22.048 distance: 97 - 103: 4.157 distance: 99 - 100: 35.632 distance: 100 - 101: 10.774 distance: 100 - 102: 24.518 distance: 103 - 104: 28.980 distance: 103 - 109: 32.004 distance: 104 - 105: 7.721 distance: 104 - 107: 30.297 distance: 105 - 106: 27.179 distance: 105 - 110: 3.816 distance: 107 - 108: 27.733 distance: 108 - 109: 26.002 distance: 110 - 111: 16.476 distance: 111 - 112: 27.036 distance: 111 - 114: 28.071 distance: 112 - 113: 14.037 distance: 112 - 118: 23.597 distance: 115 - 116: 6.630 distance: 115 - 117: 31.097 distance: 118 - 119: 27.962 distance: 119 - 120: 31.937 distance: 119 - 122: 22.098 distance: 120 - 121: 11.966 distance: 120 - 129: 27.120 distance: 122 - 123: 5.153 distance: 123 - 124: 18.182 distance: 124 - 125: 9.836 distance: 125 - 126: 7.930 distance: 126 - 127: 7.968 distance: 126 - 128: 34.385 distance: 129 - 130: 6.488 distance: 130 - 131: 24.477 distance: 130 - 133: 19.768 distance: 131 - 132: 40.169 distance: 131 - 137: 6.796 distance: 133 - 134: 22.069 distance: 134 - 135: 8.885 distance: 134 - 136: 21.125 distance: 137 - 138: 52.370 distance: 138 - 139: 36.066 distance: 139 - 140: 26.625 distance: 139 - 141: 8.671