Starting phenix.real_space_refine on Fri Mar 15 20:56:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/03_2024/6ttu_10585_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/03_2024/6ttu_10585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/03_2024/6ttu_10585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/03_2024/6ttu_10585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/03_2024/6ttu_10585_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ttu_10585/03_2024/6ttu_10585_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1 5.49 5 S 69 5.16 5 C 8099 2.51 5 N 2204 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 209": "OE1" <-> "OE2" Residue "T GLU 230": "OE1" <-> "OE2" Residue "T ASP 236": "OD1" <-> "OD2" Residue "T ARG 240": "NH1" <-> "NH2" Residue "T TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 312": "OD1" <-> "OD2" Residue "T TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 353": "OE1" <-> "OE2" Residue "T GLU 374": "OE1" <-> "OE2" Residue "T PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 402": "OD1" <-> "OD2" Residue "T ARG 403": "NH1" <-> "NH2" Residue "T ASP 492": "OD1" <-> "OD2" Residue "T ASP 515": "OD1" <-> "OD2" Residue "T ASP 525": "OD1" <-> "OD2" Residue "T GLU 553": "OE1" <-> "OE2" Residue "T ASP 574": "OD1" <-> "OD2" Residue "T PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 12": "OE1" <-> "OE2" Residue "S ASP 71": "OD1" <-> "OD2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S GLU 115": "OE1" <-> "OE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C ASP 285": "OD1" <-> "OD2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 510": "OD1" <-> "OD2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C GLU 617": "OE1" <-> "OE2" Residue "C ASP 706": "OD1" <-> "OD2" Residue "C GLU 758": "OE1" <-> "OE2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "N GLU 53": "OE1" <-> "OE2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 32": "OD1" <-> "OD2" Residue "I ASP 31": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12746 Number of models: 1 Model: "" Number of chains: 9 Chain: "T" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3085 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 67 Chain: "S" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 891 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5728 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 688} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 666 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "D" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1135 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 58 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10515 SG CYS R 42 72.537 59.783 38.458 1.00105.69 S ATOM 10534 SG CYS R 45 71.727 62.144 41.587 1.00 96.79 S ATOM 10782 SG CYS R 83 74.603 62.879 39.323 1.00114.58 S ATOM 10711 SG CYS R 75 77.674 50.473 29.345 1.00132.51 S ATOM 10878 SG CYS R 94 78.374 51.519 33.079 1.00107.60 S ATOM 10601 SG CYS R 53 73.307 67.468 39.926 1.00145.22 S ATOM 10624 SG CYS R 56 72.428 70.984 38.455 1.00149.84 S ATOM 10661 SG CYS R 68 71.603 67.584 36.570 1.00150.04 S Time building chain proxies: 6.60, per 1000 atoms: 0.52 Number of scatterers: 12746 At special positions: 0 Unit cell: (129.32, 87.98, 163.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 69 16.00 P 1 15.00 O 2370 8.00 N 2204 7.00 C 8099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS T 298 " - pdb=" SG CYS T 335 " distance=2.05 Simple disulfide: pdb=" SG CYS D 85 " - pdb=" SG CYS I 20 " distance=2.01 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: 4.97 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 6 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 14 sheets defined 44.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'T' and resid 180 through 187 Proline residue: T 185 - end of helix Processing helix chain 'T' and resid 190 through 199 removed outlier: 3.724A pdb=" N TYR T 199 " --> pdb=" O ASN T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 210 Processing helix chain 'T' and resid 213 through 221 Processing helix chain 'T' and resid 224 through 235 Processing helix chain 'T' and resid 237 through 246 Processing helix chain 'T' and resid 248 through 251 Processing helix chain 'T' and resid 266 through 288 Proline residue: T 273 - end of helix Processing helix chain 'T' and resid 533 through 537 Processing helix chain 'T' and resid 543 through 545 No H-bonds generated for 'chain 'T' and resid 543 through 545' Processing helix chain 'S' and resid 18 through 23 removed outlier: 4.573A pdb=" N GLN S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 30 Processing helix chain 'S' and resid 46 through 58 Processing helix chain 'S' and resid 69 through 75 Processing helix chain 'S' and resid 79 through 92 Processing helix chain 'S' and resid 95 through 109 Processing helix chain 'S' and resid 114 through 121 Processing helix chain 'S' and resid 131 through 137 Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 86 through 106 Processing helix chain 'C' and resid 114 through 136 Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 176 through 192 removed outlier: 4.524A pdb=" N ARG C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.880A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 253 removed outlier: 3.901A pdb=" N SER C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 277 removed outlier: 3.555A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 312 removed outlier: 3.784A pdb=" N ASP C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU C 286 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 287 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU C 297 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS C 298 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU C 301 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 308 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 334 through 358 removed outlier: 3.575A pdb=" N LYS C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 383 Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.534A pdb=" N MET C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 412' Processing helix chain 'C' and resid 417 through 430 Processing helix chain 'C' and resid 439 through 454 Processing helix chain 'C' and resid 459 through 475 Processing helix chain 'C' and resid 482 through 526 removed outlier: 7.165A pdb=" N PHE C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR C 501 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C 504 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 570 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 622 through 628 removed outlier: 4.131A pdb=" N SER C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 644 removed outlier: 4.539A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 722 Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'N' and resid 23 through 31 removed outlier: 3.547A pdb=" N VAL N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 57 No H-bonds generated for 'chain 'R' and resid 54 through 57' Processing helix chain 'R' and resid 81 through 90 removed outlier: 3.758A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 60 through 62 No H-bonds generated for 'chain 'D' and resid 60 through 62' Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.640A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 removed outlier: 4.276A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 144 removed outlier: 3.604A pdb=" N ARG D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 34 Processing helix chain 'U' and resid 38 through 40 No H-bonds generated for 'chain 'U' and resid 38 through 40' Processing helix chain 'U' and resid 56 through 59 Processing sheet with id= A, first strand: chain 'T' and resid 308 through 311 removed outlier: 3.972A pdb=" N CYS T 308 " --> pdb=" O GLY T 319 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP T 329 " --> pdb=" O CYS T 335 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS T 335 " --> pdb=" O ASP T 329 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'T' and resid 346 through 351 removed outlier: 6.623A pdb=" N GLY T 359 " --> pdb=" O LEU T 347 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU T 349 " --> pdb=" O ILE T 357 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE T 357 " --> pdb=" O LEU T 349 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR T 351 " --> pdb=" O VAL T 355 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL T 355 " --> pdb=" O TYR T 351 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP T 369 " --> pdb=" O MET T 375 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET T 375 " --> pdb=" O ASP T 369 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'T' and resid 386 through 392 removed outlier: 6.823A pdb=" N CYS T 399 " --> pdb=" O LEU T 387 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU T 389 " --> pdb=" O VAL T 397 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL T 397 " --> pdb=" O LEU T 389 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE T 391 " --> pdb=" O MET T 395 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET T 395 " --> pdb=" O PHE T 391 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER T 404 " --> pdb=" O SER T 400 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG T 420 " --> pdb=" O VAL T 407 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP T 409 " --> pdb=" O LEU T 418 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU T 418 " --> pdb=" O ASP T 409 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'T' and resid 429 through 434 removed outlier: 6.904A pdb=" N ALA T 442 " --> pdb=" O ASN T 430 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL T 432 " --> pdb=" O VAL T 440 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL T 440 " --> pdb=" O VAL T 432 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE T 434 " --> pdb=" O TYR T 438 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR T 438 " --> pdb=" O PHE T 434 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER T 443 " --> pdb=" O THR T 447 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR T 447 " --> pdb=" O SER T 443 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASN T 452 " --> pdb=" O PHE T 458 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE T 458 " --> pdb=" O ASN T 452 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 469 through 475 removed outlier: 6.774A pdb=" N GLY T 482 " --> pdb=" O ALA T 470 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU T 472 " --> pdb=" O VAL T 480 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL T 480 " --> pdb=" O LEU T 472 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR T 474 " --> pdb=" O LEU T 478 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU T 478 " --> pdb=" O TYR T 474 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG T 500 " --> pdb=" O LEU T 490 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP T 492 " --> pdb=" O CYS T 498 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N CYS T 498 " --> pdb=" O ASP T 492 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 509 through 514 removed outlier: 6.912A pdb=" N GLY T 522 " --> pdb=" O ARG T 510 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE T 512 " --> pdb=" O VAL T 520 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL T 520 " --> pdb=" O ILE T 512 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE T 514 " --> pdb=" O ARG T 518 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG T 518 " --> pdb=" O PHE T 514 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP T 532 " --> pdb=" O CYS T 547 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS T 547 " --> pdb=" O ASP T 532 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'T' and resid 560 through 563 Processing sheet with id= H, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'C' and resid 589 through 592 Processing sheet with id= J, first strand: chain 'N' and resid 12 through 17 removed outlier: 3.601A pdb=" N VAL N 70 " --> pdb=" O ARG N 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 70 through 72 Processing sheet with id= L, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.599A pdb=" N SER D 22 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 52 through 55 Processing sheet with id= N, first strand: chain 'U' and resid 12 through 16 557 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4182 1.34 - 1.47: 3008 1.47 - 1.60: 5682 1.60 - 1.72: 1 1.72 - 1.85: 99 Bond restraints: 12972 Sorted by residual: bond pdb=" O3P SEP I 32 " pdb=" P SEP I 32 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O1P SEP I 32 " pdb=" P SEP I 32 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" O2P SEP I 32 " pdb=" P SEP I 32 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CA VAL C 746 " pdb=" CB VAL C 746 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.41e+01 bond pdb=" C LEU D 89 " pdb=" N ARG D 90 " ideal model delta sigma weight residual 1.333 1.293 0.040 1.25e-02 6.40e+03 1.04e+01 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 280 106.29 - 113.22: 7220 113.22 - 120.16: 4680 120.16 - 127.09: 5223 127.09 - 134.03: 139 Bond angle restraints: 17542 Sorted by residual: angle pdb=" N LYS S 110 " pdb=" CA LYS S 110 " pdb=" C LYS S 110 " ideal model delta sigma weight residual 110.24 119.55 -9.31 1.30e+00 5.92e-01 5.13e+01 angle pdb=" C TYR C 583 " pdb=" N GLN C 584 " pdb=" CA GLN C 584 " ideal model delta sigma weight residual 122.31 112.59 9.72 2.00e+00 2.50e-01 2.36e+01 angle pdb=" N CYS C 170 " pdb=" CA CYS C 170 " pdb=" C CYS C 170 " ideal model delta sigma weight residual 113.72 107.41 6.31 1.30e+00 5.92e-01 2.36e+01 angle pdb=" N GLU C 763 " pdb=" CA GLU C 763 " pdb=" C GLU C 763 " ideal model delta sigma weight residual 108.34 114.59 -6.25 1.31e+00 5.83e-01 2.27e+01 angle pdb=" N LYS C 189 " pdb=" CA LYS C 189 " pdb=" C LYS C 189 " ideal model delta sigma weight residual 112.38 107.05 5.33 1.22e+00 6.72e-01 1.91e+01 ... (remaining 17537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6996 17.93 - 35.85: 673 35.85 - 53.78: 136 53.78 - 71.71: 32 71.71 - 89.63: 14 Dihedral angle restraints: 7851 sinusoidal: 3146 harmonic: 4705 Sorted by residual: dihedral pdb=" CB CYS D 85 " pdb=" SG CYS D 85 " pdb=" SG CYS I 20 " pdb=" CB CYS I 20 " ideal model delta sinusoidal sigma weight residual -86.00 -20.18 -65.82 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA ASP C 362 " pdb=" CB ASP C 362 " pdb=" CG ASP C 362 " pdb=" OD1 ASP C 362 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 239 " pdb=" CB ASP C 239 " pdb=" CG ASP C 239 " pdb=" OD1 ASP C 239 " ideal model delta sinusoidal sigma weight residual -30.00 -88.89 58.89 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 7848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1543 0.053 - 0.107: 394 0.107 - 0.160: 61 0.160 - 0.213: 4 0.213 - 0.267: 2 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CG LEU C 585 " pdb=" CB LEU C 585 " pdb=" CD1 LEU C 585 " pdb=" CD2 LEU C 585 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA PRO C 174 " pdb=" N PRO C 174 " pdb=" C PRO C 174 " pdb=" CB PRO C 174 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE T 448 " pdb=" N ILE T 448 " pdb=" C ILE T 448 " pdb=" CB ILE T 448 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 2001 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU U 69 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C LEU U 69 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU U 69 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL U 70 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 77 " 0.002 2.00e-02 2.50e+03 1.83e-02 5.03e+00 pdb=" CG HIS R 77 " -0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS R 77 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS R 77 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS R 77 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS R 77 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 17 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO D 18 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 18 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 18 " -0.031 5.00e-02 4.00e+02 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 3 2.03 - 2.75: 1889 2.75 - 3.46: 18808 3.46 - 4.18: 29191 4.18 - 4.90: 51611 Nonbonded interactions: 101502 Sorted by model distance: nonbonded pdb=" NZ LYS C 720 " pdb=" C GLY N 76 " model vdw 1.312 3.350 nonbonded pdb=" C GLY U 75 " pdb=" N CYS I 20 " model vdw 1.336 3.350 nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.998 2.230 nonbonded pdb=" OD1 ASP C 396 " pdb=" OH TYR C 455 " model vdw 2.112 2.440 nonbonded pdb=" OD1 ASP T 201 " pdb=" OG SER T 204 " model vdw 2.212 2.440 ... (remaining 101497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.990 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 36.980 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.006 0.095 12972 Z= 0.394 Angle : 0.880 10.205 17542 Z= 0.529 Chirality : 0.047 0.267 2004 Planarity : 0.004 0.056 2220 Dihedral : 15.099 89.634 4779 Min Nonbonded Distance : 1.312 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.29 % Allowed : 7.85 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1560 helix: -0.55 (0.18), residues: 726 sheet: -1.63 (0.33), residues: 215 loop : -3.52 (0.20), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 368 HIS 0.027 0.002 HIS R 77 PHE 0.013 0.002 PHE C 508 TYR 0.017 0.002 TYR C 377 ARG 0.005 0.000 ARG C 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 353 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8100 (mmm) cc_final: 0.7887 (mmp) REVERT: T 230 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7455 (mt-10) REVERT: T 277 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7523 (tm-30) REVERT: T 322 ASP cc_start: 0.7901 (m-30) cc_final: 0.7687 (t70) REVERT: T 440 VAL cc_start: 0.9051 (t) cc_final: 0.8835 (p) REVERT: T 581 ASP cc_start: 0.8785 (t70) cc_final: 0.8222 (p0) REVERT: S 13 ILE cc_start: 0.7421 (tp) cc_final: 0.7065 (tt) REVERT: S 48 ILE cc_start: 0.9131 (mp) cc_final: 0.8241 (mp) REVERT: S 108 MET cc_start: 0.7670 (mtp) cc_final: 0.6957 (mmp) REVERT: S 113 THR cc_start: 0.7942 (p) cc_final: 0.6983 (p) REVERT: S 122 ASN cc_start: 0.8611 (t0) cc_final: 0.8410 (t0) REVERT: C 147 ARG cc_start: 0.5345 (mmt180) cc_final: 0.3502 (mmt180) REVERT: C 188 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7979 (tm-30) REVERT: N 24 GLU cc_start: 0.8531 (tp30) cc_final: 0.8190 (tp30) REVERT: D 16 ASP cc_start: 0.7716 (m-30) cc_final: 0.7440 (t0) REVERT: D 63 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8742 (mmtp) outliers start: 4 outliers final: 1 residues processed: 357 average time/residue: 0.3157 time to fit residues: 152.5486 Evaluate side-chains 235 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 43 ASN C 214 ASN C 309 ASN C 727 HIS N 41 GLN N 49 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12972 Z= 0.186 Angle : 0.593 9.181 17542 Z= 0.309 Chirality : 0.043 0.229 2004 Planarity : 0.004 0.045 2220 Dihedral : 4.124 66.993 1729 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.04 % Allowed : 17.16 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.21), residues: 1560 helix: 0.68 (0.19), residues: 721 sheet: -0.93 (0.35), residues: 219 loop : -2.85 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 248 HIS 0.009 0.001 HIS R 82 PHE 0.014 0.001 PHE C 595 TYR 0.024 0.001 TYR T 438 ARG 0.008 0.001 ARG T 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 276 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 223 MET cc_start: 0.8099 (mmm) cc_final: 0.7857 (mmp) REVERT: T 230 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7464 (mt-10) REVERT: T 277 GLN cc_start: 0.7875 (tp-100) cc_final: 0.7432 (tm-30) REVERT: T 322 ASP cc_start: 0.7895 (m-30) cc_final: 0.7632 (t70) REVERT: T 581 ASP cc_start: 0.8760 (t70) cc_final: 0.8316 (p0) REVERT: S 108 MET cc_start: 0.7516 (mtp) cc_final: 0.6887 (mmp) REVERT: S 122 ASN cc_start: 0.8690 (t0) cc_final: 0.8480 (t0) REVERT: C 147 ARG cc_start: 0.5312 (mmt180) cc_final: 0.3836 (mmt180) REVERT: C 187 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8354 (tp) REVERT: C 681 ARG cc_start: 0.6892 (mmm-85) cc_final: 0.6376 (tpp80) REVERT: C 716 VAL cc_start: 0.8899 (p) cc_final: 0.8618 (p) REVERT: N 11 LYS cc_start: 0.8546 (tttp) cc_final: 0.8295 (ptmt) REVERT: N 14 GLU cc_start: 0.8074 (tt0) cc_final: 0.7845 (tt0) REVERT: N 24 GLU cc_start: 0.8316 (tp30) cc_final: 0.8032 (tp30) REVERT: R 23 GLU cc_start: 0.5469 (mp0) cc_final: 0.5238 (mp0) REVERT: R 76 ASN cc_start: 0.8571 (m-40) cc_final: 0.7546 (t0) REVERT: R 88 LEU cc_start: 0.8724 (mm) cc_final: 0.8337 (mm) REVERT: D 16 ASP cc_start: 0.7748 (m-30) cc_final: 0.7471 (t0) REVERT: D 60 TYR cc_start: 0.8672 (t80) cc_final: 0.8357 (t80) REVERT: D 63 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8623 (mmtp) REVERT: U 25 ASN cc_start: 0.8712 (m110) cc_final: 0.8428 (m110) outliers start: 28 outliers final: 19 residues processed: 293 average time/residue: 0.2190 time to fit residues: 94.9885 Evaluate side-chains 251 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain U residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 140 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 59 HIS N 41 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** U 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12972 Z= 0.246 Angle : 0.573 7.254 17542 Z= 0.300 Chirality : 0.042 0.211 2004 Planarity : 0.003 0.038 2220 Dihedral : 4.306 62.139 1729 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.20 % Allowed : 19.27 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1560 helix: 0.89 (0.19), residues: 721 sheet: -0.77 (0.35), residues: 223 loop : -2.48 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 248 HIS 0.009 0.001 HIS R 82 PHE 0.016 0.001 PHE T 267 TYR 0.013 0.001 TYR U 59 ARG 0.006 0.000 ARG R 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 277 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7372 (tm-30) REVERT: T 322 ASP cc_start: 0.7981 (m-30) cc_final: 0.7713 (t70) REVERT: T 448 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8647 (mt) REVERT: T 487 THR cc_start: 0.8344 (p) cc_final: 0.8052 (p) REVERT: T 581 ASP cc_start: 0.8792 (t70) cc_final: 0.8282 (p0) REVERT: S 14 PHE cc_start: 0.7553 (t80) cc_final: 0.7212 (t80) REVERT: S 108 MET cc_start: 0.7547 (mtp) cc_final: 0.6825 (mmp) REVERT: S 122 ASN cc_start: 0.8699 (t0) cc_final: 0.8453 (t0) REVERT: C 147 ARG cc_start: 0.5530 (mmt180) cc_final: 0.3898 (mmt180) REVERT: C 187 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8189 (mt) REVERT: C 322 MET cc_start: 0.8978 (tpp) cc_final: 0.8363 (ttt) REVERT: C 613 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7014 (tp40) REVERT: C 681 ARG cc_start: 0.6916 (mmm-85) cc_final: 0.6506 (tpp80) REVERT: C 716 VAL cc_start: 0.8991 (p) cc_final: 0.8779 (p) REVERT: C 724 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7537 (m) REVERT: R 76 ASN cc_start: 0.8638 (m-40) cc_final: 0.7631 (t0) REVERT: R 88 LEU cc_start: 0.8776 (mm) cc_final: 0.8448 (mm) REVERT: D 16 ASP cc_start: 0.7764 (m-30) cc_final: 0.7479 (t0) REVERT: D 63 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8617 (mmtp) REVERT: U 15 LEU cc_start: 0.8649 (mm) cc_final: 0.8412 (mp) REVERT: U 25 ASN cc_start: 0.8696 (m110) cc_final: 0.8431 (m110) outliers start: 44 outliers final: 25 residues processed: 265 average time/residue: 0.2217 time to fit residues: 87.4260 Evaluate side-chains 247 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 448 ILE Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 113 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain U residue 7 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 59 HIS C 214 ASN N 41 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12972 Z= 0.200 Angle : 0.555 10.164 17542 Z= 0.286 Chirality : 0.041 0.186 2004 Planarity : 0.003 0.054 2220 Dihedral : 4.371 59.885 1729 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.84 % Allowed : 20.51 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1560 helix: 1.01 (0.19), residues: 720 sheet: -0.58 (0.36), residues: 224 loop : -2.27 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 70 HIS 0.010 0.001 HIS R 82 PHE 0.014 0.001 PHE T 566 TYR 0.011 0.001 TYR C 366 ARG 0.005 0.000 ARG T 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 230 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7934 (mt-10) REVERT: T 277 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7449 (tm-30) REVERT: T 322 ASP cc_start: 0.7944 (m-30) cc_final: 0.7698 (t70) REVERT: T 440 VAL cc_start: 0.9077 (t) cc_final: 0.8816 (p) REVERT: S 122 ASN cc_start: 0.8640 (t0) cc_final: 0.8370 (t0) REVERT: C 147 ARG cc_start: 0.5774 (mmt180) cc_final: 0.3936 (mmt180) REVERT: C 613 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6950 (tp40) REVERT: C 681 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6689 (tpp80) REVERT: C 716 VAL cc_start: 0.8955 (p) cc_final: 0.8729 (p) REVERT: C 724 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7466 (m) REVERT: N 14 GLU cc_start: 0.8098 (tt0) cc_final: 0.7892 (tt0) REVERT: R 56 CYS cc_start: 0.1087 (OUTLIER) cc_final: 0.0833 (t) REVERT: R 76 ASN cc_start: 0.8633 (m-40) cc_final: 0.7617 (t0) REVERT: R 88 LEU cc_start: 0.8745 (mm) cc_final: 0.8431 (mm) REVERT: D 60 TYR cc_start: 0.8679 (t80) cc_final: 0.8285 (t80) REVERT: D 63 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8633 (mmtp) REVERT: U 15 LEU cc_start: 0.8576 (mm) cc_final: 0.8348 (mp) REVERT: U 25 ASN cc_start: 0.8651 (m110) cc_final: 0.8390 (m110) outliers start: 39 outliers final: 29 residues processed: 255 average time/residue: 0.2248 time to fit residues: 84.7379 Evaluate side-chains 253 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 221 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 59 HIS Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain U residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 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 206 GLN C 214 ASN C 272 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 60 ASN U 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12972 Z= 0.190 Angle : 0.533 7.905 17542 Z= 0.276 Chirality : 0.041 0.177 2004 Planarity : 0.003 0.035 2220 Dihedral : 4.376 61.057 1729 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.42 % Allowed : 21.45 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1560 helix: 1.07 (0.19), residues: 725 sheet: -0.38 (0.37), residues: 221 loop : -2.19 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 70 HIS 0.022 0.001 HIS S 59 PHE 0.017 0.001 PHE T 566 TYR 0.011 0.001 TYR C 366 ARG 0.003 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 234 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 230 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7407 (mp0) REVERT: T 277 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7467 (tm-30) REVERT: T 322 ASP cc_start: 0.7911 (m-30) cc_final: 0.7656 (t70) REVERT: S 122 ASN cc_start: 0.8573 (t0) cc_final: 0.8296 (t0) REVERT: C 32 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.5836 (t80) REVERT: C 147 ARG cc_start: 0.5874 (mmt180) cc_final: 0.3917 (mmt180) REVERT: C 322 MET cc_start: 0.8879 (tpp) cc_final: 0.8002 (ttt) REVERT: C 540 LEU cc_start: 0.9006 (mt) cc_final: 0.8795 (mp) REVERT: C 613 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6915 (tp40) REVERT: C 681 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6649 (tpp80) REVERT: C 716 VAL cc_start: 0.8952 (p) cc_final: 0.8737 (p) REVERT: N 24 GLU cc_start: 0.8305 (tp30) cc_final: 0.7985 (tp30) REVERT: R 56 CYS cc_start: 0.1094 (OUTLIER) cc_final: 0.0840 (t) REVERT: R 76 ASN cc_start: 0.8679 (m-40) cc_final: 0.7609 (t0) REVERT: R 88 LEU cc_start: 0.8738 (mm) cc_final: 0.8476 (mm) REVERT: D 16 ASP cc_start: 0.7631 (m-30) cc_final: 0.7359 (t0) REVERT: D 60 TYR cc_start: 0.8665 (t80) cc_final: 0.8316 (t80) REVERT: U 2 GLN cc_start: 0.7081 (pt0) cc_final: 0.6502 (pp30) REVERT: U 25 ASN cc_start: 0.8656 (m110) cc_final: 0.8391 (m110) outliers start: 47 outliers final: 30 residues processed: 263 average time/residue: 0.2218 time to fit residues: 85.6961 Evaluate side-chains 254 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 60 ASN Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 54 GLN C 214 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12972 Z= 0.203 Angle : 0.544 9.329 17542 Z= 0.280 Chirality : 0.041 0.213 2004 Planarity : 0.003 0.035 2220 Dihedral : 4.331 60.346 1728 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.20 % Allowed : 23.64 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1560 helix: 1.15 (0.20), residues: 718 sheet: -0.21 (0.37), residues: 217 loop : -2.12 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 70 HIS 0.007 0.001 HIS R 82 PHE 0.021 0.001 PHE T 566 TYR 0.018 0.001 TYR U 59 ARG 0.003 0.000 ARG T 245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 230 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7445 (mp0) REVERT: T 277 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7467 (tm-30) REVERT: T 322 ASP cc_start: 0.7868 (m-30) cc_final: 0.7619 (t70) REVERT: S 122 ASN cc_start: 0.8542 (t0) cc_final: 0.8156 (t0) REVERT: C 147 ARG cc_start: 0.6181 (mmt90) cc_final: 0.4076 (mmt180) REVERT: C 322 MET cc_start: 0.8855 (tpp) cc_final: 0.8000 (ttt) REVERT: C 545 TRP cc_start: 0.8648 (m100) cc_final: 0.8401 (m-10) REVERT: C 613 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6969 (tp40) REVERT: C 681 ARG cc_start: 0.7178 (mmm-85) cc_final: 0.6655 (tpp80) REVERT: C 716 VAL cc_start: 0.8973 (p) cc_final: 0.8759 (p) REVERT: N 24 GLU cc_start: 0.8327 (tp30) cc_final: 0.7999 (tp30) REVERT: R 56 CYS cc_start: 0.0948 (OUTLIER) cc_final: 0.0675 (t) REVERT: R 76 ASN cc_start: 0.8725 (m-40) cc_final: 0.7591 (t0) REVERT: R 88 LEU cc_start: 0.8726 (mm) cc_final: 0.8473 (mm) REVERT: D 16 ASP cc_start: 0.7744 (m-30) cc_final: 0.7387 (t0) REVERT: D 60 TYR cc_start: 0.8676 (t80) cc_final: 0.8250 (t80) REVERT: U 2 GLN cc_start: 0.7118 (pt0) cc_final: 0.6575 (pp30) REVERT: U 25 ASN cc_start: 0.8650 (m110) cc_final: 0.8375 (m110) outliers start: 44 outliers final: 33 residues processed: 252 average time/residue: 0.2216 time to fit residues: 82.8376 Evaluate side-chains 252 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 478 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain U residue 7 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN C 602 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12972 Z= 0.185 Angle : 0.555 9.658 17542 Z= 0.281 Chirality : 0.041 0.173 2004 Planarity : 0.003 0.036 2220 Dihedral : 4.286 58.360 1728 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.20 % Allowed : 24.07 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1560 helix: 1.20 (0.20), residues: 719 sheet: -0.06 (0.37), residues: 215 loop : -2.00 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 PHE 0.010 0.001 PHE C 95 TYR 0.012 0.001 TYR C 366 ARG 0.003 0.000 ARG T 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 231 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 277 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7476 (tm-30) REVERT: T 322 ASP cc_start: 0.7857 (m-30) cc_final: 0.7546 (t70) REVERT: T 440 VAL cc_start: 0.9098 (t) cc_final: 0.8853 (p) REVERT: S 55 TRP cc_start: 0.8330 (t60) cc_final: 0.8127 (t60) REVERT: S 122 ASN cc_start: 0.8434 (t0) cc_final: 0.8154 (t0) REVERT: C 147 ARG cc_start: 0.6204 (mmt90) cc_final: 0.4052 (mmt180) REVERT: C 150 ASP cc_start: 0.4644 (OUTLIER) cc_final: 0.3868 (m-30) REVERT: C 188 GLU cc_start: 0.8450 (tt0) cc_final: 0.8226 (tp30) REVERT: C 322 MET cc_start: 0.8821 (tpp) cc_final: 0.7960 (ttt) REVERT: C 602 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: C 681 ARG cc_start: 0.7223 (mmm-85) cc_final: 0.6614 (tpp80) REVERT: C 716 VAL cc_start: 0.8975 (p) cc_final: 0.8769 (p) REVERT: N 24 GLU cc_start: 0.8331 (tp30) cc_final: 0.8017 (tp30) REVERT: R 76 ASN cc_start: 0.8734 (m-40) cc_final: 0.7595 (t0) REVERT: R 88 LEU cc_start: 0.8732 (mm) cc_final: 0.8512 (mm) REVERT: D 16 ASP cc_start: 0.7823 (m-30) cc_final: 0.7463 (t0) REVERT: U 2 GLN cc_start: 0.7071 (pt0) cc_final: 0.6504 (pp30) REVERT: U 25 ASN cc_start: 0.8633 (m110) cc_final: 0.8351 (m110) outliers start: 44 outliers final: 30 residues processed: 255 average time/residue: 0.2326 time to fit residues: 88.8075 Evaluate side-chains 252 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 220 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 478 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 602 GLN Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain U residue 7 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 136 optimal weight: 0.0970 chunk 144 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12972 Z= 0.198 Angle : 0.563 8.664 17542 Z= 0.287 Chirality : 0.041 0.171 2004 Planarity : 0.003 0.035 2220 Dihedral : 4.302 57.318 1728 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.27 % Allowed : 24.51 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1560 helix: 1.24 (0.20), residues: 718 sheet: -0.06 (0.38), residues: 213 loop : -1.95 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 70 HIS 0.007 0.001 HIS R 82 PHE 0.014 0.001 PHE S 14 TYR 0.010 0.001 TYR C 366 ARG 0.002 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 221 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 277 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7463 (tm-30) REVERT: T 322 ASP cc_start: 0.7798 (m-30) cc_final: 0.7470 (t70) REVERT: S 122 ASN cc_start: 0.8449 (t0) cc_final: 0.8096 (t0) REVERT: C 147 ARG cc_start: 0.6351 (mmt90) cc_final: 0.4121 (mmt180) REVERT: C 150 ASP cc_start: 0.4340 (OUTLIER) cc_final: 0.3666 (m-30) REVERT: C 322 MET cc_start: 0.8835 (tpp) cc_final: 0.8018 (ttt) REVERT: C 602 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: C 681 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6721 (tpp80) REVERT: N 24 GLU cc_start: 0.8344 (tp30) cc_final: 0.8033 (tp30) REVERT: R 76 ASN cc_start: 0.8799 (m-40) cc_final: 0.7670 (t0) REVERT: R 88 LEU cc_start: 0.8739 (mm) cc_final: 0.8538 (mm) REVERT: D 16 ASP cc_start: 0.7901 (m-30) cc_final: 0.7522 (t0) REVERT: U 2 GLN cc_start: 0.7090 (pt0) cc_final: 0.6557 (pp30) REVERT: U 25 ASN cc_start: 0.8647 (m110) cc_final: 0.8352 (m110) REVERT: U 41 GLN cc_start: 0.7197 (mt0) cc_final: 0.6991 (mt0) outliers start: 45 outliers final: 34 residues processed: 247 average time/residue: 0.2236 time to fit residues: 82.0883 Evaluate side-chains 249 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 478 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 602 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12972 Z= 0.173 Angle : 0.567 8.202 17542 Z= 0.286 Chirality : 0.041 0.170 2004 Planarity : 0.003 0.035 2220 Dihedral : 4.269 56.727 1728 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.05 % Allowed : 24.95 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1560 helix: 1.35 (0.20), residues: 711 sheet: 0.13 (0.38), residues: 209 loop : -1.85 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 55 HIS 0.008 0.001 HIS R 82 PHE 0.010 0.001 PHE C 95 TYR 0.012 0.001 TYR C 366 ARG 0.003 0.000 ARG C 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 220 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 277 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7429 (tm-30) REVERT: T 322 ASP cc_start: 0.7791 (m-30) cc_final: 0.7474 (t70) REVERT: S 122 ASN cc_start: 0.8371 (t0) cc_final: 0.8092 (t0) REVERT: C 147 ARG cc_start: 0.6484 (mmt90) cc_final: 0.4246 (mmt180) REVERT: C 150 ASP cc_start: 0.4413 (OUTLIER) cc_final: 0.3627 (m-30) REVERT: C 188 GLU cc_start: 0.8538 (tp30) cc_final: 0.7951 (tp30) REVERT: C 322 MET cc_start: 0.8800 (tpp) cc_final: 0.7990 (ttt) REVERT: C 577 ARG cc_start: 0.6691 (ptt180) cc_final: 0.6271 (ptp-170) REVERT: C 633 MET cc_start: 0.7219 (ppp) cc_final: 0.5779 (mmp) REVERT: C 681 ARG cc_start: 0.7203 (mmm-85) cc_final: 0.6784 (tpp80) REVERT: N 11 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8379 (ptmt) REVERT: N 24 GLU cc_start: 0.8309 (tp30) cc_final: 0.7986 (tp30) REVERT: R 76 ASN cc_start: 0.8805 (m-40) cc_final: 0.7662 (t0) REVERT: R 88 LEU cc_start: 0.8785 (mm) cc_final: 0.8584 (mm) REVERT: D 12 ASP cc_start: 0.8364 (m-30) cc_final: 0.8138 (t0) REVERT: D 16 ASP cc_start: 0.7888 (m-30) cc_final: 0.7532 (t0) REVERT: D 60 TYR cc_start: 0.8687 (t80) cc_final: 0.8317 (t80) REVERT: D 66 LYS cc_start: 0.8543 (mttt) cc_final: 0.8290 (ttpt) REVERT: U 2 GLN cc_start: 0.7074 (pt0) cc_final: 0.6550 (pp30) REVERT: U 25 ASN cc_start: 0.8633 (m110) cc_final: 0.8356 (m110) outliers start: 42 outliers final: 34 residues processed: 245 average time/residue: 0.2352 time to fit residues: 85.7348 Evaluate side-chains 245 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 210 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 478 LEU Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12972 Z= 0.201 Angle : 0.584 9.141 17542 Z= 0.296 Chirality : 0.041 0.167 2004 Planarity : 0.003 0.036 2220 Dihedral : 4.276 54.452 1728 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.84 % Allowed : 25.16 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1560 helix: 1.35 (0.20), residues: 717 sheet: 0.09 (0.37), residues: 210 loop : -1.87 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP S 55 HIS 0.007 0.001 HIS R 82 PHE 0.015 0.001 PHE S 14 TYR 0.016 0.001 TYR T 524 ARG 0.002 0.000 ARG C 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 277 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7461 (tm-30) REVERT: T 322 ASP cc_start: 0.7793 (m-30) cc_final: 0.7483 (t70) REVERT: S 55 TRP cc_start: 0.8276 (t60) cc_final: 0.7914 (t60) REVERT: S 122 ASN cc_start: 0.8422 (t0) cc_final: 0.8120 (t0) REVERT: C 147 ARG cc_start: 0.6441 (mmt90) cc_final: 0.4194 (mmt180) REVERT: C 150 ASP cc_start: 0.4579 (OUTLIER) cc_final: 0.3784 (m-30) REVERT: C 188 GLU cc_start: 0.8517 (tp30) cc_final: 0.8206 (tp30) REVERT: C 322 MET cc_start: 0.8830 (tpp) cc_final: 0.8023 (ttt) REVERT: C 577 ARG cc_start: 0.6412 (ptt180) cc_final: 0.6045 (ptp-170) REVERT: C 611 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6457 (tp) REVERT: C 633 MET cc_start: 0.7243 (ppp) cc_final: 0.5783 (mmp) REVERT: C 681 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6774 (tpp80) REVERT: N 11 LYS cc_start: 0.8553 (ptmt) cc_final: 0.8330 (ptmt) REVERT: N 24 GLU cc_start: 0.8338 (tp30) cc_final: 0.8023 (tp30) REVERT: R 76 ASN cc_start: 0.8830 (m-40) cc_final: 0.7683 (t0) REVERT: U 2 GLN cc_start: 0.7060 (pt0) cc_final: 0.6572 (pp30) REVERT: U 25 ASN cc_start: 0.8641 (m110) cc_final: 0.8344 (m110) outliers start: 39 outliers final: 36 residues processed: 240 average time/residue: 0.2206 time to fit residues: 78.9221 Evaluate side-chains 250 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 191 HIS Chi-restraints excluded: chain T residue 286 TRP Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain T residue 335 CYS Chi-restraints excluded: chain T residue 349 LEU Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 450 VAL Chi-restraints excluded: chain T residue 451 TRP Chi-restraints excluded: chain T residue 461 THR Chi-restraints excluded: chain T residue 478 LEU Chi-restraints excluded: chain T residue 569 VAL Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 144 TRP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 649 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 108 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 602 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097682 restraints weight = 26337.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.098898 restraints weight = 19996.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099377 restraints weight = 19810.127| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12972 Z= 0.208 Angle : 0.591 8.543 17542 Z= 0.299 Chirality : 0.041 0.169 2004 Planarity : 0.003 0.034 2220 Dihedral : 4.226 45.789 1728 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.91 % Allowed : 25.09 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1560 helix: 1.34 (0.20), residues: 717 sheet: 0.18 (0.38), residues: 204 loop : -1.86 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP S 55 HIS 0.006 0.001 HIS R 82 PHE 0.019 0.001 PHE S 14 TYR 0.011 0.001 TYR T 524 ARG 0.004 0.000 ARG R 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.07 seconds wall clock time: 50 minutes 9.18 seconds (3009.18 seconds total)