Starting phenix.real_space_refine on Fri Jan 19 20:02:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5m_12040/01_2024/7b5m_12040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5m_12040/01_2024/7b5m_12040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5m_12040/01_2024/7b5m_12040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5m_12040/01_2024/7b5m_12040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5m_12040/01_2024/7b5m_12040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5m_12040/01_2024/7b5m_12040_updated.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 1 5.49 5 S 77 5.16 5 C 7934 2.51 5 N 2165 2.21 5 O 2348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C ASP 510": "OD1" <-> "OD2" Residue "C GLU 662": "OE1" <-> "OE2" Residue "H PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 499": "OE1" <-> "OE2" Residue "H TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 530": "NH1" <-> "NH2" Residue "T GLU 214": "OE1" <-> "OE2" Residue "T PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 14": "OD1" <-> "OD2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 156": "OE1" <-> "OE2" Residue "U ARG 42": "NH1" <-> "NH2" Residue "U ARG 72": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12530 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5171 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1753 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "T" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2535 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "S" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1112 Classifications: {'peptide': 140} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 677 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 1, 'DHA:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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 5383 SG CYS H 344 124.834 27.487 42.162 1.00187.92 S ATOM 5401 SG CYS H 347 124.269 24.043 44.127 1.00184.84 S ATOM 5512 SG CYS H 362 123.783 27.327 45.755 1.00183.12 S ATOM 5548 SG CYS H 367 127.110 26.277 44.967 1.00193.28 S ATOM 5584 SG CYS H 372 123.440 39.235 41.178 1.00198.39 S ATOM 5611 SG CYS H 375 126.387 39.421 38.980 1.00203.22 S ATOM 5705 SG CYS H 389 123.621 41.887 38.172 1.00185.76 S ATOM 11951 SG CYS R 42 70.704 48.988 30.551 1.00 63.26 S ATOM 11970 SG CYS R 45 70.096 47.638 34.273 1.00 71.18 S ATOM 12218 SG CYS R 83 72.706 50.193 33.564 1.00 93.25 S ATOM 12147 SG CYS R 75 74.570 51.227 16.962 1.00111.39 S ATOM 12314 SG CYS R 94 75.900 49.930 20.422 1.00 97.58 S ATOM 12037 SG CYS R 53 70.792 52.218 37.790 1.00112.66 S ATOM 12060 SG CYS R 56 68.791 55.270 38.874 1.00126.06 S ATOM 12097 SG CYS R 68 68.319 53.615 35.339 1.00134.19 S Time building chain proxies: 6.60, per 1000 atoms: 0.53 Number of scatterers: 12530 At special positions: 0 Unit cell: (153.69, 86.11, 159.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 77 16.00 P 1 15.00 O 2348 8.00 N 2165 7.00 C 7934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 367 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 362 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 347 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 344 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 382 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 375 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 372 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 389 " 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 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " 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 : 15 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB DHA P 163 " Number of C-beta restraints generated: 3004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 5 sheets defined 48.1% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'C' and resid 21 through 31 Processing helix chain 'C' and resid 39 through 53 removed outlier: 3.681A pdb=" N CYS C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 105 Processing helix chain 'C' and resid 115 through 136 removed outlier: 3.846A pdb=" N GLN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.527A pdb=" N ASP C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 187 removed outlier: 4.162A pdb=" N GLN C 178 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL C 179 " --> pdb=" O ASN C 176 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 233 through 253 removed outlier: 4.179A pdb=" N THR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 276 removed outlier: 4.083A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN C 276 " --> pdb=" O GLN C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.917A pdb=" N ASN C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 336 through 359 removed outlier: 4.010A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 359 " --> pdb=" O CYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 381 Processing helix chain 'C' and resid 391 through 403 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 417 through 430 Processing helix chain 'C' and resid 439 through 454 removed outlier: 4.332A pdb=" N ASP C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 475 Processing helix chain 'C' and resid 482 through 500 removed outlier: 7.653A pdb=" N PHE C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 527 removed outlier: 3.964A pdb=" N ILE C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 573 removed outlier: 3.525A pdb=" N GLU C 560 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C 561 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 571 " --> pdb=" O ALA C 568 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 572 " --> pdb=" O PHE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 615 removed outlier: 3.981A pdb=" N TYR C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN C 615 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 629 Processing helix chain 'C' and resid 633 through 645 Processing helix chain 'H' and resid 317 through 324 Processing helix chain 'H' and resid 332 through 340 Processing helix chain 'H' and resid 404 through 429 removed outlier: 3.741A pdb=" N ALA H 409 " --> pdb=" O GLU H 405 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA H 410 " --> pdb=" O ARG H 406 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU H 411 " --> pdb=" O SER H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 447 Processing helix chain 'H' and resid 453 through 480 removed outlier: 4.383A pdb=" N TYR H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 511 Processing helix chain 'H' and resid 518 through 549 Processing helix chain 'T' and resid 97 through 99 No H-bonds generated for 'chain 'T' and resid 97 through 99' Processing helix chain 'T' and resid 102 through 111 removed outlier: 4.031A pdb=" N CYS T 111 " --> pdb=" O GLY T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 120 Processing helix chain 'T' and resid 125 through 130 Processing helix chain 'T' and resid 149 through 157 Processing helix chain 'T' and resid 195 through 204 removed outlier: 5.073A pdb=" N GLN T 204 " --> pdb=" O GLY T 200 " (cutoff:3.500A) Processing helix chain 'T' and resid 220 through 228 removed outlier: 4.149A pdb=" N LYS T 228 " --> pdb=" O ASN T 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 245 through 254 Processing helix chain 'T' and resid 271 through 280 Processing helix chain 'T' and resid 299 through 308 Processing helix chain 'T' and resid 325 through 333 removed outlier: 3.661A pdb=" N GLN T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 358 Processing helix chain 'T' and resid 375 through 382 Processing helix chain 'K' and resid 26 through 29 No H-bonds generated for 'chain 'K' and resid 26 through 29' Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'S' and resid 25 through 32 Processing helix chain 'S' and resid 46 through 58 Processing helix chain 'S' and resid 87 through 90 No H-bonds generated for 'chain 'S' and resid 87 through 90' Processing helix chain 'S' and resid 97 through 110 Processing helix chain 'S' and resid 113 through 127 Processing helix chain 'S' and resid 132 through 138 Processing helix chain 'S' and resid 150 through 157 Processing helix chain 'U' and resid 23 through 34 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 84 through 90 Processing sheet with id= A, first strand: chain 'C' and resid 587 through 590 removed outlier: 3.514A pdb=" N LEU C 601 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'T' and resid 139 through 141 removed outlier: 6.785A pdb=" N ALA T 162 " --> pdb=" O LEU T 140 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS T 185 " --> pdb=" O PHE T 163 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN T 210 " --> pdb=" O MET T 186 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG T 234 " --> pdb=" O LEU T 211 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU T 260 " --> pdb=" O LEU T 235 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN T 287 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS T 314 " --> pdb=" O LEU T 288 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N HIS T 339 " --> pdb=" O LEU T 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'K' and resid 55 through 58 removed outlier: 4.017A pdb=" N TYR K 57 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU K 68 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.735A pdb=" N LEU S 6 " --> pdb=" O PHE S 14 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE S 14 " --> pdb=" O LEU S 6 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'U' and resid 68 through 71 removed outlier: 4.245A pdb=" N LEU U 43 " --> pdb=" O LEU U 50 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1407 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: 2.94 Time building geometry restraints manager: 5.18 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: 4107 1.34 - 1.46: 2570 1.46 - 1.58: 5977 1.58 - 1.70: 3 1.70 - 1.82: 105 Bond restraints: 12762 Sorted by residual: bond pdb=" CA DHA P 163 " pdb=" CB DHA P 163 " ideal model delta sigma weight residual 1.530 1.350 0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" OG1 TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O1P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O3P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N DHA P 163 " pdb=" CA DHA P 163 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.90e-02 2.77e+03 7.58e+00 ... (remaining 12757 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.65: 286 106.65 - 113.54: 7033 113.54 - 120.43: 5027 120.43 - 127.33: 4773 127.33 - 134.22: 133 Bond angle restraints: 17252 Sorted by residual: angle pdb=" N DHA P 163 " pdb=" CA DHA P 163 " pdb=" CB DHA P 163 " ideal model delta sigma weight residual 110.50 123.21 -12.71 1.70e+00 3.46e-01 5.59e+01 angle pdb=" N PRO S 2 " pdb=" CA PRO S 2 " pdb=" CB PRO S 2 " ideal model delta sigma weight residual 103.00 110.39 -7.39 1.10e+00 8.26e-01 4.52e+01 angle pdb=" N GLU C 335 " pdb=" CA GLU C 335 " pdb=" C GLU C 335 " ideal model delta sigma weight residual 114.62 107.55 7.07 1.14e+00 7.69e-01 3.85e+01 angle pdb=" N VAL C 591 " pdb=" CA VAL C 591 " pdb=" C VAL C 591 " ideal model delta sigma weight residual 113.53 108.35 5.18 9.80e-01 1.04e+00 2.79e+01 angle pdb=" C DHA P 163 " pdb=" CA DHA P 163 " pdb=" CB DHA P 163 " ideal model delta sigma weight residual 110.10 120.10 -10.00 1.90e+00 2.77e-01 2.77e+01 ... (remaining 17247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6829 17.94 - 35.87: 706 35.87 - 53.80: 147 53.80 - 71.74: 28 71.74 - 89.67: 14 Dihedral angle restraints: 7724 sinusoidal: 3120 harmonic: 4604 Sorted by residual: dihedral pdb=" CA ASP S 33 " pdb=" C ASP S 33 " pdb=" N LEU S 34 " pdb=" CA LEU S 34 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASP S 96 " pdb=" C ASP S 96 " pdb=" N GLN S 97 " pdb=" CA GLN S 97 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PHE C 385 " pdb=" C PHE C 385 " pdb=" N ASN C 386 " pdb=" CA ASN C 386 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 7721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1389 0.047 - 0.094: 427 0.094 - 0.141: 100 0.141 - 0.188: 15 0.188 - 0.235: 4 Chirality restraints: 1935 Sorted by residual: chirality pdb=" CA PRO S 2 " pdb=" N PRO S 2 " pdb=" C PRO S 2 " pdb=" CB PRO S 2 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU T 100 " pdb=" CB LEU T 100 " pdb=" CD1 LEU T 100 " pdb=" CD2 LEU T 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE C 684 " pdb=" CA ILE C 684 " pdb=" CG1 ILE C 684 " pdb=" CG2 ILE C 684 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1932 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 385 " 0.016 2.00e-02 2.50e+03 2.25e-02 8.86e+00 pdb=" CG PHE C 385 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE C 385 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 385 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 385 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 385 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 385 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 27 " -0.021 2.00e-02 2.50e+03 1.69e-02 7.16e+00 pdb=" CG TRP R 27 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP R 27 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP R 27 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 27 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 27 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 27 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 27 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 27 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 27 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 173 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO C 174 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " -0.036 5.00e-02 4.00e+02 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 156 2.58 - 3.16: 11093 3.16 - 3.74: 19825 3.74 - 4.32: 25840 4.32 - 4.90: 41134 Nonbonded interactions: 98048 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 2.001 2.230 nonbonded pdb=" O VAL C 227 " pdb=" OG SER C 231 " model vdw 2.210 2.440 nonbonded pdb=" OG SER C 481 " pdb=" OD1 ASP C 483 " model vdw 2.212 2.440 nonbonded pdb=" NH2 ARG T 294 " pdb=" OE1 GLU P 185 " model vdw 2.236 2.520 nonbonded pdb=" O SER H 331 " pdb=" OG SER H 334 " model vdw 2.246 2.440 ... (remaining 98043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.360 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: 0.000 Extract box with map and model: 6.680 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.480 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.180 12762 Z= 0.311 Angle : 0.866 13.687 17252 Z= 0.485 Chirality : 0.048 0.235 1935 Planarity : 0.005 0.081 2204 Dihedral : 15.580 89.674 4720 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 0.22 % Allowed : 0.58 % Favored : 99.20 % Cbeta Deviations : 0.07 % 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: -2.61 (0.20), residues: 1527 helix: -0.54 (0.18), residues: 803 sheet: -2.63 (0.60), residues: 72 loop : -3.23 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP R 27 HIS 0.010 0.002 HIS H 382 PHE 0.051 0.002 PHE C 385 TYR 0.026 0.002 TYR C 278 ARG 0.014 0.001 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 173 ARG cc_start: 0.5463 (mmm-85) cc_final: 0.5023 (mmm-85) REVERT: C 261 MET cc_start: 0.8469 (mpp) cc_final: 0.8129 (mtm) REVERT: C 537 ILE cc_start: 0.8384 (tt) cc_final: 0.8163 (tp) REVERT: C 672 TYR cc_start: 0.8404 (t80) cc_final: 0.8122 (t80) REVERT: C 675 TYR cc_start: 0.6480 (t80) cc_final: 0.5836 (t80) REVERT: T 97 TRP cc_start: 0.3785 (m100) cc_final: 0.3157 (m100) REVERT: K 38 MET cc_start: 0.6698 (mtt) cc_final: 0.6310 (mtt) REVERT: K 58 MET cc_start: 0.6429 (ptm) cc_final: 0.6074 (ptm) REVERT: U 39 ASP cc_start: 0.8380 (m-30) cc_final: 0.7945 (p0) REVERT: U 61 ILE cc_start: 0.8931 (mp) cc_final: 0.8616 (mp) outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.2582 time to fit residues: 49.2044 Evaluate side-chains 98 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain T residue 238 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 119 optimal weight: 0.0020 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN C 404 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 ASN ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 542 HIS ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 190 ASN ** T 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12762 Z= 0.162 Angle : 0.605 15.321 17252 Z= 0.319 Chirality : 0.040 0.187 1935 Planarity : 0.004 0.046 2204 Dihedral : 5.510 34.104 1678 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.95 % Allowed : 8.32 % Favored : 90.74 % Cbeta Deviations : 0.07 % 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: -1.88 (0.21), residues: 1527 helix: 0.22 (0.18), residues: 801 sheet: -2.46 (0.66), residues: 68 loop : -3.08 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 27 HIS 0.007 0.001 HIS R 48 PHE 0.024 0.001 PHE H 457 TYR 0.024 0.001 TYR H 529 ARG 0.004 0.000 ARG P 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 515 LYS cc_start: 0.8491 (mttt) cc_final: 0.8194 (mtmm) REVERT: C 585 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8841 (pp) REVERT: C 614 TYR cc_start: 0.6458 (m-80) cc_final: 0.6188 (m-80) REVERT: C 675 TYR cc_start: 0.6596 (t80) cc_final: 0.5496 (t80) REVERT: T 97 TRP cc_start: 0.4087 (m100) cc_final: 0.3358 (m100) REVERT: T 170 MET cc_start: 0.7100 (mmt) cc_final: 0.6775 (tpp) REVERT: K 38 MET cc_start: 0.6705 (mtt) cc_final: 0.6334 (mtt) REVERT: K 58 MET cc_start: 0.6192 (ptm) cc_final: 0.5973 (ptm) REVERT: U 11 LYS cc_start: 0.7257 (tttm) cc_final: 0.6821 (mttp) REVERT: U 39 ASP cc_start: 0.8442 (m-30) cc_final: 0.7890 (p0) outliers start: 13 outliers final: 8 residues processed: 120 average time/residue: 0.2641 time to fit residues: 46.3750 Evaluate side-chains 109 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain U residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 204 GLN ** T 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12762 Z= 0.299 Angle : 0.662 15.387 17252 Z= 0.351 Chirality : 0.042 0.205 1935 Planarity : 0.004 0.045 2204 Dihedral : 5.629 34.724 1675 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 1.90 % Allowed : 13.64 % Favored : 84.46 % Cbeta Deviations : 0.07 % 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: -2.00 (0.21), residues: 1527 helix: 0.10 (0.18), residues: 793 sheet: -2.58 (0.60), residues: 79 loop : -3.06 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 144 HIS 0.008 0.001 HIS C 343 PHE 0.031 0.002 PHE H 457 TYR 0.032 0.002 TYR C 278 ARG 0.009 0.001 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 535 PHE cc_start: 0.7545 (t80) cc_final: 0.7143 (t80) REVERT: C 585 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8606 (pp) REVERT: C 587 LYS cc_start: 0.8243 (pttp) cc_final: 0.7826 (mtmt) REVERT: C 614 TYR cc_start: 0.6530 (m-80) cc_final: 0.6111 (m-80) REVERT: C 675 TYR cc_start: 0.6772 (t80) cc_final: 0.5574 (t80) REVERT: T 170 MET cc_start: 0.7163 (mmt) cc_final: 0.6848 (tpp) REVERT: U 11 LYS cc_start: 0.7359 (tttm) cc_final: 0.7004 (mttp) REVERT: U 39 ASP cc_start: 0.8280 (m-30) cc_final: 0.7667 (p0) REVERT: U 52 ASP cc_start: 0.5742 (t0) cc_final: 0.5078 (p0) outliers start: 26 outliers final: 16 residues processed: 117 average time/residue: 0.2348 time to fit residues: 41.2895 Evaluate side-chains 113 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 493 ASN ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12762 Z= 0.161 Angle : 0.572 15.488 17252 Z= 0.300 Chirality : 0.040 0.191 1935 Planarity : 0.003 0.039 2204 Dihedral : 5.192 33.854 1675 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.68 % Allowed : 15.61 % Favored : 82.71 % Cbeta Deviations : 0.07 % 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: -1.53 (0.22), residues: 1527 helix: 0.60 (0.19), residues: 786 sheet: -2.43 (0.65), residues: 68 loop : -2.97 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 27 HIS 0.006 0.001 HIS C 345 PHE 0.020 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.004 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 585 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8657 (pp) REVERT: C 614 TYR cc_start: 0.6713 (m-80) cc_final: 0.6497 (m-80) REVERT: C 675 TYR cc_start: 0.7004 (t80) cc_final: 0.6098 (t80) REVERT: H 422 MET cc_start: 0.8276 (tpp) cc_final: 0.8005 (mmt) REVERT: K 11 LYS cc_start: 0.6698 (mttt) cc_final: 0.6410 (mmmt) REVERT: K 38 MET cc_start: 0.6657 (mtt) cc_final: 0.6294 (mtt) REVERT: U 11 LYS cc_start: 0.7190 (tttm) cc_final: 0.6739 (mttp) REVERT: U 39 ASP cc_start: 0.8222 (m-30) cc_final: 0.7636 (p0) REVERT: U 52 ASP cc_start: 0.5787 (t0) cc_final: 0.4938 (p0) outliers start: 23 outliers final: 12 residues processed: 116 average time/residue: 0.2279 time to fit residues: 39.9882 Evaluate side-chains 109 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain P residue 184 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN C 685 ASN ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12762 Z= 0.303 Angle : 0.656 15.504 17252 Z= 0.344 Chirality : 0.043 0.343 1935 Planarity : 0.004 0.035 2204 Dihedral : 5.417 28.572 1675 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 2.26 % Allowed : 16.70 % Favored : 81.04 % Cbeta Deviations : 0.07 % 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: -1.72 (0.21), residues: 1527 helix: 0.34 (0.18), residues: 790 sheet: -2.71 (0.58), residues: 79 loop : -2.89 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 144 HIS 0.007 0.001 HIS C 343 PHE 0.032 0.002 PHE H 457 TYR 0.027 0.002 TYR C 278 ARG 0.009 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 MET cc_start: 0.8387 (mtm) cc_final: 0.8159 (mtm) REVERT: C 585 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8634 (pp) REVERT: C 608 MET cc_start: 0.7383 (mmt) cc_final: 0.7142 (mmt) REVERT: C 614 TYR cc_start: 0.6547 (m-80) cc_final: 0.6257 (m-80) REVERT: C 675 TYR cc_start: 0.7016 (t80) cc_final: 0.6343 (t80) REVERT: K 38 MET cc_start: 0.6560 (mtt) cc_final: 0.6309 (mtt) REVERT: U 11 LYS cc_start: 0.7355 (tttm) cc_final: 0.6971 (mttp) REVERT: U 39 ASP cc_start: 0.8364 (m-30) cc_final: 0.7710 (p0) outliers start: 31 outliers final: 21 residues processed: 122 average time/residue: 0.2410 time to fit residues: 44.3885 Evaluate side-chains 115 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain H residue 330 ASP Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2099 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: