Starting phenix.real_space_refine (version: dev) on Mon Feb 20 15:31:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/02_2023/6feq_4246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/02_2023/6feq_4246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/02_2023/6feq_4246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/02_2023/6feq_4246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/02_2023/6feq_4246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/02_2023/6feq_4246_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.016 sd= 0.107 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 Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12397 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'D6T': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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 chiralities: 1 Time building chain proxies: 7.47, per 1000 atoms: 0.60 Number of scatterers: 12397 At special positions: 0 Unit cell: (102.24, 96.915, 145.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2283 8.00 N 2040 7.00 C 8006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 596 " " NAG B1001 " - " ASN B 596 " Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 2.2 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 12 sheets defined 39.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 136 through 147 removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.673A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.745A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.517A pdb=" N ASN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.683A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.302A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.744A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.629A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 3.592A pdb=" N GLU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.547A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 422 through 450 removed outlier: 3.582A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.664A pdb=" N HIS A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 478 through 497 removed outlier: 3.545A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.656A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 removed outlier: 3.601A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.507A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.595A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.581A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 removed outlier: 3.561A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.602A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.721A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.595A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.811A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.847A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.573A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.615A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 removed outlier: 3.594A pdb=" N GLU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.525A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 422 through 450 removed outlier: 3.513A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.513A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 497 Proline residue: B 485 - end of helix removed outlier: 3.574A pdb=" N VAL B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 removed outlier: 3.758A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.836A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 552 " --> pdb=" O MET B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.520A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 570' Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.631A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 616 removed outlier: 3.561A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 removed outlier: 3.631A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 68 through 71 removed outlier: 3.524A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.140A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 68 through 71 Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.005A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 19 through 24 Processing sheet with id= F, first strand: chain 'C' and resid 85 through 90 removed outlier: 5.928A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.520A pdb=" N CYS D 22 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.802A pdb=" N LYS D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 41 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 19 through 24 Processing sheet with id= J, first strand: chain 'E' and resid 85 through 90 removed outlier: 5.928A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 6 through 8 removed outlier: 3.519A pdb=" N CYS F 22 " --> pdb=" O PHE F 79 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.802A pdb=" N LYS F 45 " --> pdb=" O PHE F 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 41 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1939 1.31 - 1.44: 3587 1.44 - 1.56: 7041 1.56 - 1.69: 4 1.69 - 1.82: 106 Bond restraints: 12677 Sorted by residual: bond pdb=" C27 D6T A1002 " pdb=" C31 D6T A1002 " ideal model delta sigma weight residual 1.400 1.618 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C28 D6T A1002 " pdb=" C34 D6T A1002 " ideal model delta sigma weight residual 1.400 1.615 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C32 D6T A1002 " pdb=" C33 D6T A1002 " ideal model delta sigma weight residual 1.411 1.241 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" C19 D6T A1002 " pdb=" C20 D6T A1002 " ideal model delta sigma weight residual 1.386 1.550 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C18 D6T A1002 " pdb=" C23 D6T A1002 " ideal model delta sigma weight residual 1.388 1.542 -0.154 2.00e-02 2.50e+03 5.95e+01 ... (remaining 12672 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.32: 217 105.32 - 112.50: 6487 112.50 - 119.68: 4348 119.68 - 126.86: 5977 126.86 - 134.03: 149 Bond angle restraints: 17178 Sorted by residual: angle pdb=" C29 D6T A1002 " pdb=" C30 D6T A1002 " pdb=" N6 D6T A1002 " ideal model delta sigma weight residual 110.04 129.48 -19.44 3.00e+00 1.11e-01 4.20e+01 angle pdb=" C SER B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 120.33 125.16 -4.83 8.00e-01 1.56e+00 3.65e+01 angle pdb=" C27 D6T A1002 " pdb=" C26 D6T A1002 " pdb=" N6 D6T A1002 " ideal model delta sigma weight residual 112.58 129.64 -17.06 3.00e+00 1.11e-01 3.23e+01 angle pdb=" CA LEU A 64 " pdb=" CB LEU A 64 " pdb=" CG LEU A 64 " ideal model delta sigma weight residual 116.30 131.90 -15.60 3.50e+00 8.16e-02 1.99e+01 angle pdb=" C ILE B 63 " pdb=" N LEU B 64 " pdb=" CA LEU B 64 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 ... (remaining 17173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 7143 17.62 - 35.23: 219 35.23 - 52.85: 54 52.85 - 70.47: 8 70.47 - 88.08: 10 Dihedral angle restraints: 7434 sinusoidal: 2898 harmonic: 4536 Sorted by residual: dihedral pdb=" CA PHE A 414 " pdb=" C PHE A 414 " pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta harmonic sigma weight residual -180.00 -137.37 -42.63 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA PHE B 414 " pdb=" C PHE B 414 " pdb=" N GLY B 415 " pdb=" CA GLY B 415 " ideal model delta harmonic sigma weight residual -180.00 -137.92 -42.08 0 5.00e+00 4.00e-02 7.08e+01 dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual -86.00 -19.98 -66.02 1 1.00e+01 1.00e-02 5.70e+01 ... (remaining 7431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1299 0.052 - 0.104: 529 0.104 - 0.156: 103 0.156 - 0.209: 18 0.209 - 0.261: 5 Chirality restraints: 1954 Sorted by residual: chirality pdb=" CG LEU A 565 " pdb=" CB LEU A 565 " pdb=" CD1 LEU A 565 " pdb=" CD2 LEU A 565 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA THR C 94 " pdb=" N THR C 94 " pdb=" C THR C 94 " pdb=" CB THR C 94 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1951 not shown) Planarity restraints: 2143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 63 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ILE B 63 " 0.075 2.00e-02 2.50e+03 pdb=" O ILE B 63 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 64 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 63 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ILE A 63 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE A 63 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A 64 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 87 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.98e+00 pdb=" N PRO F 88 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.034 5.00e-02 4.00e+02 ... (remaining 2140 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3512 2.80 - 3.32: 11112 3.32 - 3.85: 19932 3.85 - 4.37: 23388 4.37 - 4.90: 39995 Nonbonded interactions: 97939 Sorted by model distance: nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.271 2.440 nonbonded pdb=" OG SER E 63 " pdb=" OG SER E 74 " model vdw 2.276 2.440 nonbonded pdb=" OG SER C 63 " pdb=" OG SER C 74 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.277 2.440 nonbonded pdb=" O SER B 486 " pdb=" OG1 THR B 490 " model vdw 2.281 2.440 ... (remaining 97934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 654 or resid 1001)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8006 2.51 5 N 2040 2.21 5 O 2283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 3.840 Check model and map are aligned: 0.200 Process input model: 35.040 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.011 0.218 12677 Z= 0.716 Angle : 1.045 19.441 17178 Z= 0.549 Chirality : 0.056 0.261 1954 Planarity : 0.006 0.061 2141 Dihedral : 10.443 88.082 4517 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.17 (0.16), residues: 1558 helix: -3.35 (0.11), residues: 602 sheet: -1.64 (0.30), residues: 252 loop : -2.54 (0.20), residues: 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.2970 time to fit residues: 102.5080 Evaluate side-chains 109 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 0.0170 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 109 ASN A 116 ASN A 222 ASN A 243 HIS A 375 HIS A 425 ASN A 436 ASN A 437 GLN A 583 HIS B 41 ASN B 68 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS B 425 ASN B 437 GLN B 457 HIS B 583 HIS C 6 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN F 40 GLN F 77 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12677 Z= 0.170 Angle : 0.674 11.595 17178 Z= 0.334 Chirality : 0.042 0.184 1954 Planarity : 0.004 0.051 2141 Dihedral : 6.412 67.939 1729 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.96 (0.20), residues: 1558 helix: -0.60 (0.18), residues: 630 sheet: -1.24 (0.30), residues: 268 loop : -1.94 (0.23), residues: 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.503 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 185 average time/residue: 0.2287 time to fit residues: 63.1477 Evaluate side-chains 118 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1164 time to fit residues: 3.7089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 243 HIS A 457 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 12677 Z= 0.309 Angle : 0.684 13.270 17178 Z= 0.339 Chirality : 0.043 0.174 1954 Planarity : 0.004 0.049 2141 Dihedral : 5.944 60.691 1729 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1558 helix: 0.39 (0.20), residues: 644 sheet: -1.03 (0.30), residues: 264 loop : -1.73 (0.24), residues: 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.415 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 143 average time/residue: 0.2030 time to fit residues: 45.9903 Evaluate side-chains 121 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1350 time to fit residues: 6.4680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 12677 Z= 0.230 Angle : 0.618 12.010 17178 Z= 0.304 Chirality : 0.041 0.174 1954 Planarity : 0.003 0.045 2141 Dihedral : 5.719 60.373 1729 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.33 % 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: -0.57 (0.22), residues: 1558 helix: 0.92 (0.21), residues: 642 sheet: -0.84 (0.30), residues: 262 loop : -1.47 (0.25), residues: 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.607 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 131 average time/residue: 0.2076 time to fit residues: 43.5514 Evaluate side-chains 107 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1145 time to fit residues: 2.8437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.0060 chunk 84 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12677 Z= 0.172 Angle : 0.597 11.798 17178 Z= 0.291 Chirality : 0.041 0.203 1954 Planarity : 0.003 0.046 2141 Dihedral : 5.498 60.080 1729 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.26 % 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: -0.24 (0.22), residues: 1558 helix: 1.21 (0.21), residues: 638 sheet: -0.66 (0.31), residues: 262 loop : -1.28 (0.25), residues: 658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.718 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 127 average time/residue: 0.2019 time to fit residues: 41.2349 Evaluate side-chains 108 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1189 time to fit residues: 3.6671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.0040 chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.0770 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.8156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12677 Z= 0.199 Angle : 0.597 12.072 17178 Z= 0.292 Chirality : 0.041 0.199 1954 Planarity : 0.003 0.046 2141 Dihedral : 5.415 58.804 1729 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.74 % 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: -0.08 (0.22), residues: 1558 helix: 1.38 (0.21), residues: 638 sheet: -0.56 (0.31), residues: 262 loop : -1.27 (0.25), residues: 658 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.728 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 112 average time/residue: 0.1990 time to fit residues: 35.8990 Evaluate side-chains 103 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2232 time to fit residues: 2.9443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 12677 Z= 0.277 Angle : 0.638 13.583 17178 Z= 0.312 Chirality : 0.042 0.235 1954 Planarity : 0.003 0.046 2141 Dihedral : 5.467 57.233 1729 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.37 % 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: 0.06 (0.22), residues: 1558 helix: 1.43 (0.21), residues: 642 sheet: -0.52 (0.31), residues: 262 loop : -1.12 (0.25), residues: 654 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.465 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 110 average time/residue: 0.1936 time to fit residues: 34.6940 Evaluate side-chains 96 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.505 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1168 time to fit residues: 2.3249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 582 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 12677 Z= 0.267 Angle : 0.622 13.334 17178 Z= 0.307 Chirality : 0.042 0.223 1954 Planarity : 0.003 0.048 2141 Dihedral : 5.485 57.104 1729 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.44 % 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: 0.15 (0.22), residues: 1558 helix: 1.50 (0.21), residues: 642 sheet: -0.54 (0.31), residues: 262 loop : -1.03 (0.25), residues: 654 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.396 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 111 average time/residue: 0.2181 time to fit residues: 38.5002 Evaluate side-chains 99 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1260 time to fit residues: 2.3815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 138 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 12677 Z= 0.153 Angle : 0.599 12.982 17178 Z= 0.290 Chirality : 0.041 0.261 1954 Planarity : 0.003 0.047 2141 Dihedral : 5.293 59.040 1729 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.30 % 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: 0.33 (0.22), residues: 1558 helix: 1.68 (0.21), residues: 638 sheet: -0.39 (0.32), residues: 262 loop : -0.96 (0.25), residues: 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.693 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 121 average time/residue: 0.2064 time to fit residues: 39.5919 Evaluate side-chains 105 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1118 time to fit residues: 2.3032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 12 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12677 Z= 0.176 Angle : 0.611 13.166 17178 Z= 0.297 Chirality : 0.041 0.249 1954 Planarity : 0.003 0.049 2141 Dihedral : 5.220 58.222 1729 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1558 helix: 1.58 (0.21), residues: 654 sheet: -0.39 (0.31), residues: 272 loop : -1.02 (0.26), residues: 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.577 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2324 time to fit residues: 38.8250 Evaluate side-chains 101 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068020 restraints weight = 34335.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070352 restraints weight = 16527.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071815 restraints weight = 10268.067| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 12677 Z= 0.138 Angle : 0.593 12.466 17178 Z= 0.285 Chirality : 0.040 0.265 1954 Planarity : 0.003 0.049 2141 Dihedral : 5.064 59.653 1729 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.15 % 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: 0.39 (0.22), residues: 1558 helix: 1.65 (0.21), residues: 654 sheet: -0.28 (0.31), residues: 272 loop : -0.95 (0.26), residues: 632 =============================================================================== Job complete usr+sys time: 2044.66 seconds wall clock time: 38 minutes 51.52 seconds (2331.52 seconds total)