Starting phenix.real_space_refine on Sat Feb 17 16:01:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w72_32336/02_2024/7w72_32336_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w72_32336/02_2024/7w72_32336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w72_32336/02_2024/7w72_32336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w72_32336/02_2024/7w72_32336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w72_32336/02_2024/7w72_32336_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w72_32336/02_2024/7w72_32336_updated.pdb" } resolution = 3.1 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= 0.003 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 Ca 1 9.91 5 P 1 5.49 5 S 80 5.16 5 C 12526 2.51 5 N 3167 2.21 5 O 3413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U GLU 65": "OE1" <-> "OE2" Residue "U GLU 125": "OE1" <-> "OE2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U GLU 132": "OE1" <-> "OE2" Residue "U ARG 353": "NH1" <-> "NH2" Residue "S GLU 12": "OE1" <-> "OE2" Residue "S GLU 40": "OE1" <-> "OE2" Residue "S GLU 72": "OE1" <-> "OE2" Residue "S GLU 197": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S GLU 248": "OE1" <-> "OE2" Residue "S GLU 379": "OE1" <-> "OE2" Residue "S ARG 384": "NH1" <-> "NH2" Residue "S GLU 416": "OE1" <-> "OE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 493": "OE1" <-> "OE2" Residue "S GLU 499": "OE1" <-> "OE2" Residue "T ARG 31": "NH1" <-> "NH2" Residue "T ARG 67": "NH1" <-> "NH2" Residue "T GLU 129": "OE1" <-> "OE2" Residue "T GLU 179": "OE1" <-> "OE2" Residue "T ARG 223": "NH1" <-> "NH2" Residue "T ARG 227": "NH1" <-> "NH2" Residue "T GLU 277": "OE1" <-> "OE2" Residue "T ARG 279": "NH1" <-> "NH2" Residue "T GLU 292": "OE1" <-> "OE2" Residue "T ARG 340": "NH1" <-> "NH2" Residue "T ARG 356": "NH1" <-> "NH2" Residue "T GLU 447": "OE1" <-> "OE2" Residue "T GLU 455": "OE1" <-> "OE2" Residue "T GLU 488": "OE1" <-> "OE2" Residue "T GLU 511": "OE1" <-> "OE2" Residue "K ARG 39": "NH1" <-> "NH2" Residue "K ARG 122": "NH1" <-> "NH2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "K GLU 182": "OE1" <-> "OE2" Residue "K GLU 188": "OE1" <-> "OE2" Residue "K GLU 198": "OE1" <-> "OE2" Residue "K GLU 213": "OE1" <-> "OE2" Residue "K ARG 287": "NH1" <-> "NH2" Residue "K ARG 293": "NH1" <-> "NH2" Residue "K GLU 311": "OE1" <-> "OE2" Residue "K GLU 315": "OE1" <-> "OE2" Residue "K GLU 341": "OE1" <-> "OE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19188 Number of models: 1 Model: "" Number of chains: 10 Chain: "U" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3427 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 400} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4150 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 31, 'TRANS': 501} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "T" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4268 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 40, 'TRANS': 486} Chain: "K" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2676 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 19, 'TRANS': 310} Chain breaks: 1 Chain: "A" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4557 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain breaks: 1 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'8JY': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.23, per 1000 atoms: 0.53 Number of scatterers: 19188 At special positions: 0 Unit cell: (94.64, 120.64, 166.4, 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) Ca 1 19.99 S 80 16.00 P 1 15.00 O 3413 8.00 N 3167 7.00 C 12526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS T 182 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 195 " - pdb=" SG CYS T 272 " distance=2.03 Simple disulfide: pdb=" SG CYS T 226 " - pdb=" SG CYS T 231 " distance=2.05 Simple disulfide: pdb=" SG CYS K 275 " - pdb=" SG CYS K 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 266 " distance=2.02 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=1, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG N 1 " - " ASN A 203 " " NAG S 601 " - " ASN S 267 " " NAG T 601 " - " ASN T 327 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.01 Conformation dependent library (CDL) restraints added in 3.5 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 12 sheets defined 42.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'U' and resid 3 through 21 removed outlier: 4.201A pdb=" N LEU U 7 " --> pdb=" O ALA U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 30 Processing helix chain 'U' and resid 41 through 53 Processing helix chain 'U' and resid 67 through 75 removed outlier: 3.643A pdb=" N PHE U 75 " --> pdb=" O TYR U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 116 removed outlier: 4.049A pdb=" N LEU U 116 " --> pdb=" O LEU U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 145 Processing helix chain 'U' and resid 148 through 155 Processing helix chain 'U' and resid 160 through 176 Processing helix chain 'U' and resid 179 through 193 Processing helix chain 'U' and resid 198 through 211 Proline residue: U 202 - end of helix Processing helix chain 'U' and resid 220 through 248 removed outlier: 3.834A pdb=" N LEU U 248 " --> pdb=" O SER U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 252 through 263 removed outlier: 4.447A pdb=" N PHE U 260 " --> pdb=" O ALA U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 275 through 279 Processing helix chain 'U' and resid 286 through 307 removed outlier: 4.064A pdb=" N VAL U 297 " --> pdb=" O PHE U 293 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE U 298 " --> pdb=" O GLN U 294 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR U 300 " --> pdb=" O ASN U 296 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR U 301 " --> pdb=" O VAL U 297 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE U 302 " --> pdb=" O PHE U 298 " (cutoff:3.500A) Proline residue: U 303 - end of helix Processing helix chain 'U' and resid 312 through 325 Processing helix chain 'U' and resid 332 through 348 removed outlier: 3.616A pdb=" N LEU U 337 " --> pdb=" O GLY U 333 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR U 338 " --> pdb=" O ASP U 334 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE U 341 " --> pdb=" O LEU U 337 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE U 342 " --> pdb=" O TYR U 338 " (cutoff:3.500A) Proline residue: U 343 - end of helix removed outlier: 5.101A pdb=" N HIS U 347 " --> pdb=" O PRO U 343 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU U 348 " --> pdb=" O VAL U 344 " (cutoff:3.500A) Processing helix chain 'U' and resid 355 through 377 Proline residue: U 370 - end of helix Processing helix chain 'U' and resid 384 through 417 Processing helix chain 'S' and resid 8 through 29 Processing helix chain 'S' and resid 31 through 39 Processing helix chain 'S' and resid 50 through 55 removed outlier: 3.552A pdb=" N ASN S 55 " --> pdb=" O ILE S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 118 removed outlier: 4.085A pdb=" N GLU S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 129 Processing helix chain 'S' and resid 131 through 133 No H-bonds generated for 'chain 'S' and resid 131 through 133' Processing helix chain 'S' and resid 180 through 193 Processing helix chain 'S' and resid 199 through 204 removed outlier: 4.325A pdb=" N ALA S 203 " --> pdb=" O VAL S 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 265 removed outlier: 4.512A pdb=" N GLN S 256 " --> pdb=" O ARG S 252 " (cutoff:3.500A) Proline residue: S 257 - end of helix removed outlier: 4.321A pdb=" N ALA S 264 " --> pdb=" O ASN S 260 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALA S 265 " --> pdb=" O ALA S 261 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 302 Proline residue: S 301 - end of helix No H-bonds generated for 'chain 'S' and resid 297 through 302' Processing helix chain 'S' and resid 305 through 310 removed outlier: 3.637A pdb=" N ARG S 310 " --> pdb=" O PRO S 306 " (cutoff:3.500A) Processing helix chain 'S' and resid 331 through 333 No H-bonds generated for 'chain 'S' and resid 331 through 333' Processing helix chain 'S' and resid 382 through 396 removed outlier: 3.767A pdb=" N VAL S 388 " --> pdb=" O ARG S 384 " (cutoff:3.500A) Processing helix chain 'S' and resid 420 through 451 Processing helix chain 'S' and resid 459 through 479 Processing helix chain 'S' and resid 484 through 502 Processing helix chain 'S' and resid 505 through 507 No H-bonds generated for 'chain 'S' and resid 505 through 507' Processing helix chain 'S' and resid 515 through 519 removed outlier: 3.686A pdb=" N PHE S 519 " --> pdb=" O ASP S 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 515 through 519' Processing helix chain 'S' and resid 523 through 538 Proline residue: S 528 - end of helix removed outlier: 4.298A pdb=" N VAL S 531 " --> pdb=" O LEU S 527 " (cutoff:3.500A) Proline residue: S 532 - end of helix removed outlier: 3.818A pdb=" N LEU S 537 " --> pdb=" O ILE S 533 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 removed outlier: 3.841A pdb=" N LEU T 76 " --> pdb=" O ALA T 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE T 77 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER T 78 " --> pdb=" O GLY T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 138 Processing helix chain 'T' and resid 142 through 144 No H-bonds generated for 'chain 'T' and resid 142 through 144' Processing helix chain 'T' and resid 183 through 191 Proline residue: T 188 - end of helix Processing helix chain 'T' and resid 200 through 204 removed outlier: 3.954A pdb=" N VAL T 203 " --> pdb=" O GLY T 200 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU T 204 " --> pdb=" O LEU T 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 200 through 204' Processing helix chain 'T' and resid 207 through 210 No H-bonds generated for 'chain 'T' and resid 207 through 210' Processing helix chain 'T' and resid 260 through 264 Processing helix chain 'T' and resid 343 through 345 No H-bonds generated for 'chain 'T' and resid 343 through 345' Processing helix chain 'T' and resid 397 through 399 No H-bonds generated for 'chain 'T' and resid 397 through 399' Processing helix chain 'T' and resid 453 through 455 No H-bonds generated for 'chain 'T' and resid 453 through 455' Processing helix chain 'T' and resid 491 through 493 No H-bonds generated for 'chain 'T' and resid 491 through 493' Processing helix chain 'T' and resid 526 through 547 Processing helix chain 'K' and resid 59 through 75 Processing helix chain 'K' and resid 79 through 81 No H-bonds generated for 'chain 'K' and resid 79 through 81' Processing helix chain 'K' and resid 123 through 125 No H-bonds generated for 'chain 'K' and resid 123 through 125' Processing helix chain 'K' and resid 128 through 136 Processing helix chain 'K' and resid 180 through 192 Processing helix chain 'K' and resid 208 through 210 No H-bonds generated for 'chain 'K' and resid 208 through 210' Processing helix chain 'K' and resid 250 through 259 removed outlier: 3.796A pdb=" N GLU K 259 " --> pdb=" O GLU K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 270 No H-bonds generated for 'chain 'K' and resid 268 through 270' Processing helix chain 'K' and resid 300 through 302 No H-bonds generated for 'chain 'K' and resid 300 through 302' Processing helix chain 'K' and resid 351 through 356 removed outlier: 3.600A pdb=" N HIS K 356 " --> pdb=" O ALA K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 385 Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.808A pdb=" N LEU A 310 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 311 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 346 Processing helix chain 'A' and resid 371 through 397 Proline residue: A 376 - end of helix removed outlier: 4.329A pdb=" N LEU A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 447 removed outlier: 4.582A pdb=" N ALA A 429 " --> pdb=" O SER A 426 " (cutoff:3.500A) Proline residue: A 430 - end of helix removed outlier: 3.803A pdb=" N VAL A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 481 through 484 removed outlier: 3.521A pdb=" N ARG A 484 " --> pdb=" O ASN A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'A' and resid 494 through 516 Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.757A pdb=" N THR A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Proline residue: A 530 - end of helix Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 553 through 568 removed outlier: 3.548A pdb=" N GLN A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 595 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 607 through 618 Processing sheet with id= A, first strand: chain 'S' and resid 167 through 171 removed outlier: 6.308A pdb=" N THR S 143 " --> pdb=" O ALA S 168 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL S 170 " --> pdb=" O THR S 143 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR S 145 " --> pdb=" O VAL S 170 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS S 99 " --> pdb=" O LEU S 59 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU S 61 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS S 101 " --> pdb=" O LEU S 61 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL S 63 " --> pdb=" O LYS S 101 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG S 103 " --> pdb=" O VAL S 63 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL S 65 " --> pdb=" O ARG S 103 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLN S 105 " --> pdb=" O VAL S 65 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL S 67 " --> pdb=" O GLN S 105 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 271 through 276 removed outlier: 7.800A pdb=" N THR S 230 " --> pdb=" O PRO S 320 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU S 322 " --> pdb=" O THR S 230 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER S 232 " --> pdb=" O LEU S 322 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE S 324 " --> pdb=" O SER S 232 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU S 234 " --> pdb=" O PHE S 324 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU S 326 " --> pdb=" O LEU S 234 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY S 358 " --> pdb=" O LEU S 325 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR S 327 " --> pdb=" O GLY S 358 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET S 360 " --> pdb=" O TYR S 327 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 241 through 244 removed outlier: 5.894A pdb=" N VAL S 376 " --> pdb=" O ASP S 242 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR S 244 " --> pdb=" O VAL S 376 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL S 378 " --> pdb=" O TYR S 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'S' and resid 285 through 287 removed outlier: 3.916A pdb=" N SER S 292 " --> pdb=" O ASP S 287 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 171 through 176 removed outlier: 9.575A pdb=" N ARG T 83 " --> pdb=" O PRO T 224 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLU T 32 " --> pdb=" O SER T 276 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER T 278 " --> pdb=" O GLU T 32 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU T 34 " --> pdb=" O SER T 278 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL T 280 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE T 36 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL T 282 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR T 302 " --> pdb=" O ILE T 317 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 353 through 359 removed outlier: 3.644A pdb=" N VAL T 442 " --> pdb=" O THR T 370 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN T 445 " --> pdb=" O TYR T 396 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'T' and resid 503 through 509 removed outlier: 4.129A pdb=" N LEU T 474 " --> pdb=" O PRO T 382 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR T 413 " --> pdb=" O LEU T 431 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 464 through 466 Processing sheet with id= I, first strand: chain 'K' and resid 82 through 86 removed outlier: 6.941A pdb=" N ALA K 47 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N MET K 85 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU K 49 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU K 198 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE K 159 " --> pdb=" O GLU K 198 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU K 200 " --> pdb=" O ILE K 159 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET K 161 " --> pdb=" O LEU K 200 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE K 202 " --> pdb=" O MET K 161 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N GLY K 163 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP K 204 " --> pdb=" O GLY K 163 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 169 through 172 Processing sheet with id= K, first strand: chain 'A' and resid 102 through 111 removed outlier: 6.389A pdb=" N ALA A 218 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL A 145 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLN A 220 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 12.468A pdb=" N THR A 147 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N ALA A 222 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 315 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 318 through 322 790 hydrogen bonds defined for protein. 2241 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: 6.37 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5796 1.34 - 1.46: 4260 1.46 - 1.58: 9506 1.58 - 1.70: 7 1.70 - 1.83: 134 Bond restraints: 19703 Sorted by residual: bond pdb=" N PRO T 224 " pdb=" CA PRO T 224 " ideal model delta sigma weight residual 1.472 1.696 -0.224 1.21e-02 6.83e+03 3.43e+02 bond pdb=" C ARG T 223 " pdb=" N PRO T 224 " ideal model delta sigma weight residual 1.333 1.450 -0.117 1.01e-02 9.80e+03 1.33e+02 bond pdb=" O07 8JY U 501 " pdb=" P13 8JY U 501 " ideal model delta sigma weight residual 1.660 1.818 -0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" C SER K 217 " pdb=" N PRO K 218 " ideal model delta sigma weight residual 1.334 1.497 -0.163 2.34e-02 1.83e+03 4.85e+01 bond pdb=" O14 8JY U 501 " pdb=" P13 8JY U 501 " ideal model delta sigma weight residual 1.624 1.745 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 19698 not shown) Histogram of bond angle deviations from ideal: 92.80 - 102.24: 80 102.24 - 111.67: 9626 111.67 - 121.11: 12005 121.11 - 130.54: 5038 130.54 - 139.98: 113 Bond angle restraints: 26862 Sorted by residual: angle pdb=" C ARG T 223 " pdb=" N PRO T 224 " pdb=" CA PRO T 224 " ideal model delta sigma weight residual 120.23 139.98 -19.75 1.23e+00 6.61e-01 2.58e+02 angle pdb=" C VAL K 228 " pdb=" CA VAL K 228 " pdb=" CB VAL K 228 " ideal model delta sigma weight residual 111.88 130.93 -19.05 1.28e+00 6.10e-01 2.22e+02 angle pdb=" C SER K 217 " pdb=" N PRO K 218 " pdb=" CA PRO K 218 " ideal model delta sigma weight residual 119.84 137.57 -17.73 1.25e+00 6.40e-01 2.01e+02 angle pdb=" N PRO T 224 " pdb=" CA PRO T 224 " pdb=" C PRO T 224 " ideal model delta sigma weight residual 110.50 92.80 17.70 1.57e+00 4.06e-01 1.27e+02 angle pdb=" N LEU T 423 " pdb=" CA LEU T 423 " pdb=" CB LEU T 423 " ideal model delta sigma weight residual 110.98 96.63 14.35 1.32e+00 5.74e-01 1.18e+02 ... (remaining 26857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 10869 22.32 - 44.64: 715 44.64 - 66.96: 106 66.96 - 89.27: 45 89.27 - 111.59: 13 Dihedral angle restraints: 11748 sinusoidal: 4683 harmonic: 7065 Sorted by residual: dihedral pdb=" C VAL K 228 " pdb=" N VAL K 228 " pdb=" CA VAL K 228 " pdb=" CB VAL K 228 " ideal model delta harmonic sigma weight residual -122.00 -157.26 35.26 0 2.50e+00 1.60e-01 1.99e+02 dihedral pdb=" N VAL K 228 " pdb=" C VAL K 228 " pdb=" CA VAL K 228 " pdb=" CB VAL K 228 " ideal model delta harmonic sigma weight residual 123.40 151.76 -28.36 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" CB CYS T 226 " pdb=" SG CYS T 226 " pdb=" SG CYS T 231 " pdb=" CB CYS T 231 " ideal model delta sinusoidal sigma weight residual -86.00 -2.40 -83.60 1 1.00e+01 1.00e-02 8.53e+01 ... (remaining 11745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 3077 0.254 - 0.507: 10 0.507 - 0.761: 0 0.761 - 1.015: 0 1.015 - 1.268: 1 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA VAL K 228 " pdb=" N VAL K 228 " pdb=" C VAL K 228 " pdb=" CB VAL K 228 " both_signs ideal model delta sigma weight residual False 2.44 1.17 1.27 2.00e-01 2.50e+01 4.02e+01 chirality pdb=" CA PRO T 224 " pdb=" N PRO T 224 " pdb=" C PRO T 224 " pdb=" CB PRO T 224 " both_signs ideal model delta sigma weight residual False 2.72 3.18 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA GLU T 184 " pdb=" N GLU T 184 " pdb=" C GLU T 184 " pdb=" CB GLU T 184 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 3085 not shown) Planarity restraints: 3363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR U 195 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO U 196 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO U 196 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO U 196 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 245 " -0.028 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP S 245 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP S 245 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP S 245 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP S 245 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP S 245 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP S 245 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 245 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 245 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP S 245 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP U 376 " -0.022 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP U 376 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP U 376 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP U 376 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP U 376 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP U 376 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP U 376 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP U 376 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP U 376 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP U 376 " -0.003 2.00e-02 2.50e+03 ... (remaining 3360 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 213 2.61 - 3.18: 16776 3.18 - 3.75: 31308 3.75 - 4.33: 44730 4.33 - 4.90: 73217 Nonbonded interactions: 166244 Sorted by model distance: nonbonded pdb=" O ARG A 313 " pdb=" NH2 ARG A 352 " model vdw 2.032 2.520 nonbonded pdb=" O TRP T 391 " pdb=" CE3 TRP T 391 " model vdw 2.090 3.340 nonbonded pdb=" OG SER T 156 " pdb=" OE1 GLU T 429 " model vdw 2.107 2.440 nonbonded pdb=" O ASP K 115 " pdb=" OD1 ASP K 115 " model vdw 2.147 3.040 nonbonded pdb=" OE1 GLN A 297 " pdb=" OG SER A 519 " model vdw 2.158 2.440 ... (remaining 166239 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.640 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 53.000 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.007 0.224 19703 Z= 0.426 Angle : 0.912 19.745 26862 Z= 0.538 Chirality : 0.058 1.268 3088 Planarity : 0.005 0.113 3360 Dihedral : 15.941 111.593 7161 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.31 % Favored : 91.65 % Rotamer: Outliers : 0.39 % Allowed : 1.25 % Favored : 98.36 % Cbeta Deviations : 0.31 % 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: -1.15 (0.17), residues: 2384 helix: 0.32 (0.16), residues: 1039 sheet: -0.80 (0.27), residues: 389 loop : -1.94 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP S 245 HIS 0.006 0.001 HIS S 175 PHE 0.035 0.002 PHE U 315 TYR 0.036 0.002 TYR A 175 ARG 0.012 0.001 ARG S 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 295 time to evaluate : 2.173 Fit side-chains revert: symmetry clash REVERT: U 281 MET cc_start: 0.7706 (tpt) cc_final: 0.7317 (tpt) REVERT: S 269 SER cc_start: 0.7748 (t) cc_final: 0.7516 (t) REVERT: S 529 MET cc_start: 0.2020 (ttp) cc_final: 0.1095 (mtt) REVERT: A 439 LEU cc_start: 0.8295 (tt) cc_final: 0.7939 (mt) outliers start: 8 outliers final: 4 residues processed: 301 average time/residue: 0.3344 time to fit residues: 151.8627 Evaluate side-chains 225 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 213 GLU Chi-restraints excluded: chain K residue 281 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.0980 chunk 180 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.0770 chunk 96 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 113 optimal weight: 0.1980 chunk 138 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 319 GLN U 398 GLN S 114 HIS ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 149 ASN ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 424 GLN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 ASN K 207 GLN A 355 GLN A 449 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19703 Z= 0.178 Angle : 0.607 10.332 26862 Z= 0.302 Chirality : 0.042 0.189 3088 Planarity : 0.005 0.110 3360 Dihedral : 8.650 98.626 2757 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.92 % Favored : 93.04 % Rotamer: Outliers : 1.06 % Allowed : 6.71 % Favored : 92.23 % 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: -0.79 (0.17), residues: 2384 helix: 0.78 (0.16), residues: 1033 sheet: -0.86 (0.26), residues: 391 loop : -1.81 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP S 245 HIS 0.007 0.001 HIS T 65 PHE 0.021 0.001 PHE U 315 TYR 0.018 0.001 TYR K 212 ARG 0.005 0.000 ARG T 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 529 MET cc_start: 0.1739 (ttp) cc_final: 0.0871 (mtt) REVERT: T 325 MET cc_start: 0.7673 (tpp) cc_final: 0.7389 (tpp) REVERT: T 344 ASN cc_start: 0.7863 (p0) cc_final: 0.7630 (p0) REVERT: T 367 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 534 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8462 (pp) outliers start: 22 outliers final: 14 residues processed: 262 average time/residue: 0.2845 time to fit residues: 117.7538 Evaluate side-chains 244 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 229 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 209 GLN Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain A residue 534 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 216 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 214 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 527 ASN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19703 Z= 0.245 Angle : 0.597 9.637 26862 Z= 0.297 Chirality : 0.042 0.186 3088 Planarity : 0.005 0.106 3360 Dihedral : 7.289 86.896 2750 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.78 % Allowed : 8.63 % Favored : 89.58 % 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: -0.58 (0.18), residues: 2384 helix: 0.97 (0.17), residues: 1031 sheet: -0.89 (0.26), residues: 396 loop : -1.66 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP S 245 HIS 0.005 0.001 HIS T 426 PHE 0.020 0.001 PHE U 315 TYR 0.022 0.001 TYR K 59 ARG 0.004 0.000 ARG S 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 291 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: A 534 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8471 (pp) outliers start: 37 outliers final: 25 residues processed: 259 average time/residue: 0.2961 time to fit residues: 121.8465 Evaluate side-chains 251 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 224 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain U residue 381 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN K 107 ASN K 207 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19703 Z= 0.223 Angle : 0.585 9.985 26862 Z= 0.289 Chirality : 0.042 0.201 3088 Planarity : 0.005 0.107 3360 Dihedral : 6.747 83.281 2750 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.41 % Allowed : 9.89 % Favored : 87.70 % 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: -0.50 (0.18), residues: 2384 helix: 1.05 (0.17), residues: 1031 sheet: -0.85 (0.25), residues: 391 loop : -1.62 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 245 HIS 0.006 0.001 HIS T 426 PHE 0.019 0.001 PHE T 381 TYR 0.024 0.001 TYR K 59 ARG 0.003 0.000 ARG K 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 228 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 119 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6560 (tt) REVERT: S 179 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7590 (m-10) REVERT: S 529 MET cc_start: 0.1952 (tmm) cc_final: 0.0073 (mtt) REVERT: T 325 MET cc_start: 0.7816 (tpp) cc_final: 0.7542 (tpp) REVERT: T 479 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8796 (p) REVERT: T 526 TYR cc_start: 0.7443 (t80) cc_final: 0.7225 (t80) REVERT: K 291 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: A 534 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8486 (pp) outliers start: 50 outliers final: 34 residues processed: 260 average time/residue: 0.2864 time to fit residues: 118.9120 Evaluate side-chains 269 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 160 CYS Chi-restraints excluded: chain U residue 334 ASP Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain U residue 381 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 179 PHE Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 430 MET Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 582 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN K 107 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19703 Z= 0.296 Angle : 0.611 9.582 26862 Z= 0.303 Chirality : 0.043 0.191 3088 Planarity : 0.005 0.105 3360 Dihedral : 6.745 91.903 2750 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.65 % Allowed : 11.00 % Favored : 86.35 % 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: -0.52 (0.17), residues: 2384 helix: 1.02 (0.17), residues: 1030 sheet: -0.91 (0.25), residues: 396 loop : -1.59 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 245 HIS 0.006 0.001 HIS T 426 PHE 0.019 0.001 PHE U 315 TYR 0.027 0.001 TYR K 59 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 222 time to evaluate : 2.184 Fit side-chains revert: symmetry clash REVERT: S 119 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6580 (tt) REVERT: S 206 ASP cc_start: 0.6637 (t0) cc_final: 0.6293 (t0) REVERT: S 529 MET cc_start: 0.2064 (tmm) cc_final: 0.0161 (mtt) REVERT: T 479 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8808 (p) REVERT: T 526 TYR cc_start: 0.7459 (t80) cc_final: 0.7238 (t80) REVERT: K 291 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: A 534 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8500 (pp) outliers start: 55 outliers final: 36 residues processed: 256 average time/residue: 0.2799 time to fit residues: 114.4123 Evaluate side-chains 258 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 218 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 334 ASP Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain U residue 381 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 582 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.0270 chunk 207 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.0770 chunk 230 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 0.0030 chunk 120 optimal weight: 2.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 545 ASN K 45 ASN K 107 ASN K 173 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19703 Z= 0.167 Angle : 0.564 10.012 26862 Z= 0.278 Chirality : 0.041 0.182 3088 Planarity : 0.005 0.104 3360 Dihedral : 6.319 79.248 2750 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.46 % Allowed : 11.72 % Favored : 85.82 % 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: -0.37 (0.18), residues: 2384 helix: 1.19 (0.17), residues: 1031 sheet: -0.88 (0.26), residues: 387 loop : -1.55 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 376 HIS 0.005 0.001 HIS T 426 PHE 0.018 0.001 PHE T 381 TYR 0.020 0.001 TYR K 59 ARG 0.006 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 244 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 62 MET cc_start: 0.7677 (tmm) cc_final: 0.7455 (ttm) REVERT: S 119 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6504 (tt) REVERT: S 206 ASP cc_start: 0.6684 (t0) cc_final: 0.6294 (t0) REVERT: S 529 MET cc_start: 0.2227 (tmm) cc_final: 0.0203 (mtt) REVERT: T 325 MET cc_start: 0.7720 (tpp) cc_final: 0.7457 (tpp) REVERT: T 479 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8791 (p) REVERT: T 526 TYR cc_start: 0.7338 (t80) cc_final: 0.7112 (t80) REVERT: K 291 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: A 460 GLU cc_start: 0.6340 (mm-30) cc_final: 0.6000 (mm-30) REVERT: A 534 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8510 (pp) outliers start: 51 outliers final: 33 residues processed: 275 average time/residue: 0.2934 time to fit residues: 130.3965 Evaluate side-chains 266 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 334 ASP Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 398 GLN ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19703 Z= 0.202 Angle : 0.573 10.636 26862 Z= 0.281 Chirality : 0.041 0.178 3088 Planarity : 0.005 0.102 3360 Dihedral : 6.211 78.241 2750 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.41 % Allowed : 12.78 % Favored : 84.80 % 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: -0.31 (0.18), residues: 2384 helix: 1.23 (0.17), residues: 1031 sheet: -0.87 (0.25), residues: 387 loop : -1.50 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 376 HIS 0.005 0.001 HIS T 426 PHE 0.018 0.001 PHE T 381 TYR 0.022 0.001 TYR K 59 ARG 0.006 0.000 ARG S 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 1 MET cc_start: 0.4165 (ttp) cc_final: 0.3938 (ttm) REVERT: S 62 MET cc_start: 0.7694 (tmm) cc_final: 0.7456 (ttm) REVERT: S 119 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6521 (tt) REVERT: S 206 ASP cc_start: 0.6805 (t0) cc_final: 0.6413 (t0) REVERT: S 529 MET cc_start: 0.2411 (tmm) cc_final: 0.0331 (mtt) REVERT: T 325 MET cc_start: 0.7723 (tpp) cc_final: 0.7458 (tpp) REVERT: T 479 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8822 (p) REVERT: K 291 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: A 460 GLU cc_start: 0.6364 (mm-30) cc_final: 0.5978 (mm-30) REVERT: A 534 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8522 (pp) outliers start: 50 outliers final: 39 residues processed: 264 average time/residue: 0.2879 time to fit residues: 121.2040 Evaluate side-chains 270 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 334 ASP Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 270 VAL Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 268 MET Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.0170 chunk 91 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 347 HIS ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 516 ASN K 45 ASN K 107 ASN A 592 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19703 Z= 0.183 Angle : 0.562 10.808 26862 Z= 0.276 Chirality : 0.041 0.174 3088 Planarity : 0.005 0.104 3360 Dihedral : 6.046 78.725 2750 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.41 % Allowed : 12.98 % Favored : 84.61 % 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: -0.28 (0.18), residues: 2384 helix: 1.27 (0.17), residues: 1034 sheet: -0.86 (0.25), residues: 390 loop : -1.51 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 376 HIS 0.005 0.001 HIS T 426 PHE 0.017 0.001 PHE T 381 TYR 0.021 0.001 TYR K 59 ARG 0.008 0.000 ARG S 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 232 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 1 MET cc_start: 0.4158 (ttp) cc_final: 0.3947 (ttm) REVERT: S 62 MET cc_start: 0.7669 (tmm) cc_final: 0.7431 (ttm) REVERT: S 119 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6457 (tt) REVERT: S 206 ASP cc_start: 0.6767 (t0) cc_final: 0.6349 (t0) REVERT: S 529 MET cc_start: 0.2413 (tmm) cc_final: 0.0303 (mtt) REVERT: T 325 MET cc_start: 0.7683 (tpp) cc_final: 0.7394 (tpp) REVERT: T 479 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8817 (p) REVERT: K 291 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: A 460 GLU cc_start: 0.6314 (mm-30) cc_final: 0.5953 (mm-30) REVERT: A 534 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8515 (pp) outliers start: 50 outliers final: 38 residues processed: 264 average time/residue: 0.2784 time to fit residues: 118.4029 Evaluate side-chains 266 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 224 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 334 ASP Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 270 VAL Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 202 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 347 HIS ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19703 Z= 0.217 Angle : 0.574 11.378 26862 Z= 0.282 Chirality : 0.041 0.172 3088 Planarity : 0.005 0.101 3360 Dihedral : 6.011 77.816 2750 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.41 % Allowed : 12.88 % Favored : 84.71 % 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: -0.26 (0.18), residues: 2384 helix: 1.28 (0.17), residues: 1034 sheet: -0.85 (0.25), residues: 390 loop : -1.49 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 245 HIS 0.006 0.001 HIS T 426 PHE 0.018 0.001 PHE T 381 TYR 0.023 0.001 TYR K 59 ARG 0.008 0.000 ARG S 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 2.368 Fit side-chains revert: symmetry clash REVERT: U 1 MET cc_start: 0.4144 (ttp) cc_final: 0.3923 (ttm) REVERT: S 62 MET cc_start: 0.7678 (tmm) cc_final: 0.7435 (ttm) REVERT: S 119 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6496 (tt) REVERT: S 206 ASP cc_start: 0.6818 (t0) cc_final: 0.6410 (t0) REVERT: S 529 MET cc_start: 0.2430 (tmm) cc_final: 0.0307 (mtt) REVERT: T 344 ASN cc_start: 0.7873 (p0) cc_final: 0.7642 (p0) REVERT: T 479 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8825 (p) REVERT: K 291 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: A 460 GLU cc_start: 0.6306 (mm-30) cc_final: 0.5944 (mm-30) REVERT: A 534 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8533 (pp) outliers start: 50 outliers final: 40 residues processed: 258 average time/residue: 0.2774 time to fit residues: 115.7439 Evaluate side-chains 267 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 334 ASP Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 270 VAL Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 157 optimal weight: 0.0570 chunk 237 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 347 HIS ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 462 HIS K 45 ASN K 107 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19703 Z= 0.172 Angle : 0.557 11.565 26862 Z= 0.272 Chirality : 0.041 0.170 3088 Planarity : 0.005 0.103 3360 Dihedral : 5.838 79.416 2750 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.12 % Allowed : 13.22 % Favored : 84.66 % 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: -0.20 (0.18), residues: 2384 helix: 1.36 (0.17), residues: 1033 sheet: -0.82 (0.26), residues: 382 loop : -1.50 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 376 HIS 0.005 0.001 HIS T 426 PHE 0.017 0.001 PHE T 381 TYR 0.019 0.001 TYR K 59 ARG 0.009 0.000 ARG S 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 62 MET cc_start: 0.7673 (tmm) cc_final: 0.7460 (ttm) REVERT: S 119 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6463 (tt) REVERT: S 206 ASP cc_start: 0.6776 (t0) cc_final: 0.6357 (t0) REVERT: S 517 GLN cc_start: 0.5658 (tp40) cc_final: 0.4996 (mt0) REVERT: S 529 MET cc_start: 0.2422 (tmm) cc_final: 0.0292 (mtt) REVERT: T 344 ASN cc_start: 0.7855 (p0) cc_final: 0.7608 (p0) REVERT: T 479 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8818 (p) REVERT: K 291 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: A 460 GLU cc_start: 0.6247 (mm-30) cc_final: 0.5998 (mm-30) REVERT: A 534 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8527 (pp) outliers start: 44 outliers final: 37 residues processed: 264 average time/residue: 0.2955 time to fit residues: 126.6400 Evaluate side-chains 264 residues out of total 2079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 334 ASP Chi-restraints excluded: chain U residue 376 TRP Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 121 SER Chi-restraints excluded: chain S residue 175 HIS Chi-restraints excluded: chain S residue 182 ILE Chi-restraints excluded: chain S residue 270 VAL Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 364 VAL Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 408 CYS Chi-restraints excluded: chain T residue 118 ASP Chi-restraints excluded: chain T residue 175 VAL Chi-restraints excluded: chain T residue 182 CYS Chi-restraints excluded: chain T residue 183 THR Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 263 MET Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 349 VAL Chi-restraints excluded: chain T residue 370 THR Chi-restraints excluded: chain T residue 372 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 443 SER Chi-restraints excluded: chain T residue 479 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 282 SER Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 194 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 347 HIS ** S 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 462 HIS ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.087372 restraints weight = 28755.399| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.02 r_work: 0.2857 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19703 Z= 0.165 Angle : 0.557 11.226 26862 Z= 0.271 Chirality : 0.041 0.172 3088 Planarity : 0.005 0.099 3360 Dihedral : 5.706 80.318 2750 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.17 % Allowed : 13.22 % Favored : 84.61 % 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: -0.17 (0.18), residues: 2384 helix: 1.37 (0.17), residues: 1036 sheet: -0.76 (0.26), residues: 380 loop : -1.48 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 376 HIS 0.006 0.001 HIS T 426 PHE 0.016 0.001 PHE T 381 TYR 0.019 0.001 TYR K 59 ARG 0.009 0.000 ARG S 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4035.16 seconds wall clock time: 74 minutes 46.13 seconds (4486.13 seconds total)