Starting phenix.real_space_refine on Thu Jan 18 08:08:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs4_34220/01_2024/8gs4_34220.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs4_34220/01_2024/8gs4_34220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs4_34220/01_2024/8gs4_34220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs4_34220/01_2024/8gs4_34220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs4_34220/01_2024/8gs4_34220.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs4_34220/01_2024/8gs4_34220.pdb" } resolution = 3.5 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= 0.001 sd= 0.085 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5288 2.51 5 N 1412 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8250 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4125 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 34, 'TRANS': 490} Chain breaks: 3 Chain: "B" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4125 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 34, 'TRANS': 490} Chain breaks: 3 Time building chain proxies: 4.87, per 1000 atoms: 0.59 Number of scatterers: 8250 At special positions: 0 Unit cell: (65.32, 153.64, 81.88, 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 36 16.00 O 1514 8.00 N 1412 7.00 C 5288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 34.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.564A pdb=" N THR A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 removed outlier: 3.716A pdb=" N THR A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.859A pdb=" N ASP A 197 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.981A pdb=" N GLY A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.893A pdb=" N GLY A 220 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 221 " --> pdb=" O VAL A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 221' Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.598A pdb=" N LEU A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.799A pdb=" N ASN A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.759A pdb=" N TYR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 405 through 417 removed outlier: 4.100A pdb=" N VAL A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.596A pdb=" N LEU A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 4.163A pdb=" N ARG A 441 " --> pdb=" O TRP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 460 removed outlier: 3.923A pdb=" N HIS A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 459 " --> pdb=" O PHE A 455 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 460' Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.536A pdb=" N LEU A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.635A pdb=" N VAL A 513 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 545 removed outlier: 4.160A pdb=" N LEU A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 542 " --> pdb=" O TRP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.628A pdb=" N LEU A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.971A pdb=" N LEU A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 609' Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.564A pdb=" N THR B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.716A pdb=" N THR B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.859A pdb=" N ASP B 197 " --> pdb=" O ASN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.981A pdb=" N GLY B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.892A pdb=" N GLY B 220 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 221 " --> pdb=" O VAL B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 221' Processing helix chain 'B' and resid 232 through 248 removed outlier: 3.599A pdb=" N LEU B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.799A pdb=" N ASN B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 273' Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.758A pdb=" N TYR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.504A pdb=" N MET B 368 " --> pdb=" O PRO B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 removed outlier: 4.091A pdb=" N VAL B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN B 412 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.596A pdb=" N LEU B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 4.163A pdb=" N ARG B 441 " --> pdb=" O TRP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 453 Processing helix chain 'B' and resid 454 through 460 removed outlier: 3.924A pdb=" N HIS B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 459 " --> pdb=" O PHE B 455 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 460' Processing helix chain 'B' and resid 463 through 474 removed outlier: 3.534A pdb=" N LEU B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.636A pdb=" N VAL B 513 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 545 removed outlier: 4.160A pdb=" N LEU B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 533 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 542 " --> pdb=" O TRP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 604 removed outlier: 3.626A pdb=" N LEU B 604 " --> pdb=" O PHE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 removed outlier: 3.966A pdb=" N LEU B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 609' Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 57 removed outlier: 3.720A pdb=" N VAL A 66 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.213A pdb=" N ALA A 210 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS A 177 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU A 257 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL A 179 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE A 259 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 181 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.213A pdb=" N ALA A 210 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE A 262 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU A 181 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 290 removed outlier: 8.448A pdb=" N PHE A 483 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 382 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 46 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.720A pdb=" N VAL B 66 " --> pdb=" O ARG B 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 210 removed outlier: 4.213A pdb=" N ALA B 210 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS B 177 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU B 257 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL B 179 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE B 259 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU B 181 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 210 removed outlier: 4.213A pdb=" N ALA B 210 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE B 262 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 181 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 290 removed outlier: 8.448A pdb=" N PHE B 483 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 382 " --> pdb=" O PHE B 483 " (cutoff:3.500A) 157 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2713 1.34 - 1.46: 2003 1.46 - 1.58: 3706 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 8480 Sorted by residual: bond pdb=" CG LEU A 581 " pdb=" CD1 LEU A 581 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.46e+00 bond pdb=" CG LEU B 581 " pdb=" CD1 LEU B 581 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.46e+00 bond pdb=" C GLN B 549 " pdb=" N PRO B 550 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.56e+00 bond pdb=" C GLN A 549 " pdb=" N PRO A 550 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.56e+00 bond pdb=" CA ASP A 440 " pdb=" CB ASP A 440 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.62e-02 3.81e+03 9.59e-01 ... (remaining 8475 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.61: 343 106.61 - 113.52: 4411 113.52 - 120.42: 3292 120.42 - 127.33: 3388 127.33 - 134.24: 118 Bond angle restraints: 11552 Sorted by residual: angle pdb=" N VAL B 359 " pdb=" CA VAL B 359 " pdb=" C VAL B 359 " ideal model delta sigma weight residual 113.53 108.90 4.63 9.80e-01 1.04e+00 2.23e+01 angle pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" C VAL A 359 " ideal model delta sigma weight residual 113.53 108.90 4.63 9.80e-01 1.04e+00 2.23e+01 angle pdb=" C VAL A 461 " pdb=" N ALA A 462 " pdb=" CA ALA A 462 " ideal model delta sigma weight residual 121.80 112.76 9.04 2.44e+00 1.68e-01 1.37e+01 angle pdb=" C VAL B 461 " pdb=" N ALA B 462 " pdb=" CA ALA B 462 " ideal model delta sigma weight residual 121.80 112.76 9.04 2.44e+00 1.68e-01 1.37e+01 angle pdb=" C GLY A 545 " pdb=" N ASP A 546 " pdb=" CA ASP A 546 " ideal model delta sigma weight residual 120.69 110.52 10.17 2.95e+00 1.15e-01 1.19e+01 ... (remaining 11547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 4370 15.56 - 31.11: 496 31.11 - 46.67: 108 46.67 - 62.22: 14 62.22 - 77.78: 4 Dihedral angle restraints: 4992 sinusoidal: 1970 harmonic: 3022 Sorted by residual: dihedral pdb=" CA ALA A 462 " pdb=" C ALA A 462 " pdb=" N PRO A 463 " pdb=" CA PRO A 463 " ideal model delta harmonic sigma weight residual 180.00 141.19 38.81 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CA ALA B 462 " pdb=" C ALA B 462 " pdb=" N PRO B 463 " pdb=" CA PRO B 463 " ideal model delta harmonic sigma weight residual 180.00 141.19 38.81 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CB CYS B 317 " pdb=" SG CYS B 317 " pdb=" SG CYS B 328 " pdb=" CB CYS B 328 " ideal model delta sinusoidal sigma weight residual 93.00 153.84 -60.84 1 1.00e+01 1.00e-02 4.92e+01 ... (remaining 4989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 637 0.031 - 0.063: 383 0.063 - 0.094: 127 0.094 - 0.126: 74 0.126 - 0.157: 15 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CB THR A 101 " pdb=" CA THR A 101 " pdb=" OG1 THR A 101 " pdb=" CG2 THR A 101 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CB THR B 101 " pdb=" CA THR B 101 " pdb=" OG1 THR B 101 " pdb=" CG2 THR B 101 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA LEU A 581 " pdb=" N LEU A 581 " pdb=" C LEU A 581 " pdb=" CB LEU A 581 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1233 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 462 " 0.064 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO A 463 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 462 " 0.064 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO B 463 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 298 " 0.021 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP B 298 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 298 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 298 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 298 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 298 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 298 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 298 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 298 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 298 " 0.003 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2002 2.78 - 3.31: 7699 3.31 - 3.84: 12585 3.84 - 4.37: 14988 4.37 - 4.90: 25900 Nonbonded interactions: 63174 Sorted by model distance: nonbonded pdb=" OG SER A 269 " pdb=" OG SER A 299 " model vdw 2.251 2.440 nonbonded pdb=" OG SER B 269 " pdb=" OG SER B 299 " model vdw 2.252 2.440 nonbonded pdb=" O GLU A 327 " pdb=" NH2 ARG A 331 " model vdw 2.255 2.520 nonbonded pdb=" O GLU B 327 " pdb=" NH2 ARG B 331 " model vdw 2.255 2.520 nonbonded pdb=" O SER B 575 " pdb=" NZ LYS B 578 " model vdw 2.271 2.520 ... (remaining 63169 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.050 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 24.190 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.004 0.052 8480 Z= 0.265 Angle : 0.833 10.174 11552 Z= 0.441 Chirality : 0.048 0.157 1236 Planarity : 0.007 0.097 1518 Dihedral : 13.581 77.781 3042 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -4.70 (0.22), residues: 1034 helix: -3.64 (0.23), residues: 266 sheet: -3.45 (0.45), residues: 110 loop : -2.97 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP B 298 HIS 0.006 0.001 HIS B 582 PHE 0.026 0.002 PHE B 262 TYR 0.017 0.002 TYR B 580 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.927 Fit side-chains REVERT: A 260 THR cc_start: 0.8752 (m) cc_final: 0.8511 (p) REVERT: B 260 THR cc_start: 0.8739 (m) cc_final: 0.8499 (p) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1884 time to fit residues: 30.4883 Evaluate side-chains 94 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8480 Z= 0.289 Angle : 0.755 8.824 11552 Z= 0.382 Chirality : 0.047 0.152 1236 Planarity : 0.006 0.098 1518 Dihedral : 6.607 39.726 1140 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 1.15 % Allowed : 8.39 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -4.35 (0.22), residues: 1034 helix: -3.04 (0.25), residues: 260 sheet: -3.41 (0.45), residues: 110 loop : -2.87 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 298 HIS 0.006 0.001 HIS A 458 PHE 0.020 0.002 PHE B 262 TYR 0.015 0.001 TYR B 214 ARG 0.002 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.973 Fit side-chains REVERT: A 227 GLN cc_start: 0.6602 (tp-100) cc_final: 0.6310 (tp-100) REVERT: B 227 GLN cc_start: 0.6610 (tp-100) cc_final: 0.6314 (tp-100) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.1784 time to fit residues: 27.5665 Evaluate side-chains 104 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8480 Z= 0.316 Angle : 0.750 8.782 11552 Z= 0.379 Chirality : 0.047 0.136 1236 Planarity : 0.006 0.096 1518 Dihedral : 6.591 40.251 1140 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 2.30 % Allowed : 15.40 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -4.19 (0.23), residues: 1034 helix: -2.78 (0.27), residues: 260 sheet: -3.38 (0.44), residues: 106 loop : -2.82 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 298 HIS 0.007 0.001 HIS A 458 PHE 0.022 0.002 PHE A 262 TYR 0.016 0.002 TYR B 481 ARG 0.003 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.840 Fit side-chains REVERT: A 133 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6736 (t80) REVERT: A 227 GLN cc_start: 0.6506 (tp-100) cc_final: 0.6195 (tp-100) REVERT: A 236 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5143 (pp) REVERT: A 503 GLU cc_start: 0.7151 (pm20) cc_final: 0.5953 (tm-30) REVERT: B 133 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6732 (t80) REVERT: B 227 GLN cc_start: 0.6513 (tp-100) cc_final: 0.6205 (tp-100) REVERT: B 236 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5144 (pp) REVERT: B 503 GLU cc_start: 0.7155 (pm20) cc_final: 0.5952 (tm-30) outliers start: 20 outliers final: 12 residues processed: 107 average time/residue: 0.1720 time to fit residues: 26.7976 Evaluate side-chains 109 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8480 Z= 0.179 Angle : 0.662 7.730 11552 Z= 0.328 Chirality : 0.044 0.142 1236 Planarity : 0.006 0.085 1518 Dihedral : 5.868 39.330 1140 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 2.76 % Allowed : 17.59 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -3.79 (0.24), residues: 1034 helix: -2.33 (0.30), residues: 254 sheet: -3.12 (0.45), residues: 106 loop : -2.62 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 570 HIS 0.003 0.001 HIS A 582 PHE 0.011 0.001 PHE A 483 TYR 0.010 0.001 TYR A 481 ARG 0.002 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.850 Fit side-chains REVERT: A 133 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6517 (t80) REVERT: A 147 TYR cc_start: 0.8404 (m-80) cc_final: 0.8159 (m-10) REVERT: A 448 ARG cc_start: 0.6086 (ttt180) cc_final: 0.5785 (ttm-80) REVERT: B 133 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6511 (t80) REVERT: B 147 TYR cc_start: 0.8410 (m-80) cc_final: 0.8166 (m-10) REVERT: B 448 ARG cc_start: 0.6086 (ttt180) cc_final: 0.5780 (ttm-80) outliers start: 24 outliers final: 10 residues processed: 112 average time/residue: 0.1840 time to fit residues: 30.0500 Evaluate side-chains 98 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8480 Z= 0.338 Angle : 0.749 8.935 11552 Z= 0.379 Chirality : 0.047 0.147 1236 Planarity : 0.006 0.095 1518 Dihedral : 6.404 40.307 1140 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 4.83 % Allowed : 17.93 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -3.76 (0.24), residues: 1034 helix: -2.31 (0.31), residues: 240 sheet: -3.52 (0.41), residues: 118 loop : -2.49 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 570 HIS 0.008 0.002 HIS A 458 PHE 0.024 0.002 PHE A 262 TYR 0.018 0.002 TYR B 481 ARG 0.003 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 96 time to evaluate : 0.921 Fit side-chains REVERT: A 133 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6685 (t80) REVERT: A 227 GLN cc_start: 0.6540 (tp-100) cc_final: 0.6292 (tp-100) REVERT: B 133 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6680 (t80) REVERT: B 227 GLN cc_start: 0.6547 (tp-100) cc_final: 0.6295 (tp-100) outliers start: 42 outliers final: 30 residues processed: 124 average time/residue: 0.1809 time to fit residues: 32.6450 Evaluate side-chains 127 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8480 Z= 0.207 Angle : 0.674 8.975 11552 Z= 0.339 Chirality : 0.044 0.139 1236 Planarity : 0.006 0.087 1518 Dihedral : 5.965 40.004 1140 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 4.60 % Allowed : 20.34 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -3.63 (0.24), residues: 1034 helix: -2.13 (0.31), residues: 250 sheet: -3.20 (0.44), residues: 106 loop : -2.52 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 570 HIS 0.004 0.001 HIS A 458 PHE 0.014 0.001 PHE A 262 TYR 0.013 0.001 TYR B 418 ARG 0.003 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 90 time to evaluate : 0.998 Fit side-chains REVERT: A 102 LEU cc_start: 0.8153 (mm) cc_final: 0.7831 (mt) REVERT: A 133 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6659 (t80) REVERT: A 190 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: A 368 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5611 (ttt) REVERT: A 446 MET cc_start: 0.5189 (OUTLIER) cc_final: 0.4913 (ttt) REVERT: A 448 ARG cc_start: 0.6080 (ttt180) cc_final: 0.5779 (ttm-80) REVERT: B 102 LEU cc_start: 0.8148 (mm) cc_final: 0.7827 (mt) REVERT: B 133 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6657 (t80) REVERT: B 190 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: B 446 MET cc_start: 0.5180 (OUTLIER) cc_final: 0.4907 (ttt) REVERT: B 448 ARG cc_start: 0.6083 (ttt180) cc_final: 0.5778 (ttm-80) outliers start: 40 outliers final: 23 residues processed: 115 average time/residue: 0.1756 time to fit residues: 29.2646 Evaluate side-chains 115 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 84 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8480 Z= 0.298 Angle : 0.723 9.320 11552 Z= 0.367 Chirality : 0.047 0.182 1236 Planarity : 0.006 0.091 1518 Dihedral : 6.215 40.364 1140 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 5.17 % Allowed : 20.46 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -3.62 (0.24), residues: 1034 helix: -2.13 (0.32), residues: 240 sheet: -3.48 (0.41), residues: 118 loop : -2.41 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 570 HIS 0.007 0.001 HIS A 458 PHE 0.021 0.002 PHE A 262 TYR 0.018 0.002 TYR B 481 ARG 0.003 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 88 time to evaluate : 0.941 Fit side-chains REVERT: A 102 LEU cc_start: 0.8160 (mm) cc_final: 0.7850 (mt) REVERT: A 133 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6665 (t80) REVERT: A 368 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5877 (ttt) REVERT: A 446 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5188 (ttt) REVERT: B 102 LEU cc_start: 0.8146 (mm) cc_final: 0.7850 (mt) REVERT: B 133 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6660 (t80) REVERT: B 446 MET cc_start: 0.5440 (OUTLIER) cc_final: 0.5189 (ttt) outliers start: 45 outliers final: 32 residues processed: 116 average time/residue: 0.1725 time to fit residues: 29.4060 Evaluate side-chains 125 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 88 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8480 Z= 0.245 Angle : 0.703 9.970 11552 Z= 0.356 Chirality : 0.045 0.171 1236 Planarity : 0.006 0.088 1518 Dihedral : 6.029 40.286 1140 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 4.48 % Allowed : 21.95 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -3.54 (0.24), residues: 1034 helix: -2.04 (0.32), residues: 240 sheet: -3.14 (0.45), residues: 106 loop : -2.47 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 570 HIS 0.005 0.001 HIS B 458 PHE 0.017 0.002 PHE A 262 TYR 0.014 0.001 TYR B 481 ARG 0.003 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 0.988 Fit side-chains REVERT: A 102 LEU cc_start: 0.8145 (mm) cc_final: 0.7853 (mt) REVERT: A 133 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6667 (t80) REVERT: A 368 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.5837 (ttt) REVERT: B 102 LEU cc_start: 0.8137 (mm) cc_final: 0.7837 (mt) REVERT: B 133 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.6660 (t80) outliers start: 39 outliers final: 28 residues processed: 118 average time/residue: 0.1635 time to fit residues: 28.3903 Evaluate side-chains 120 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8480 Z= 0.297 Angle : 0.735 10.587 11552 Z= 0.372 Chirality : 0.046 0.169 1236 Planarity : 0.006 0.091 1518 Dihedral : 6.197 40.298 1140 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.83 % Favored : 86.17 % Rotamer: Outliers : 4.48 % Allowed : 22.41 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -3.58 (0.24), residues: 1034 helix: -2.03 (0.32), residues: 240 sheet: -3.43 (0.42), residues: 118 loop : -2.42 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 570 HIS 0.006 0.001 HIS B 458 PHE 0.020 0.002 PHE A 262 TYR 0.017 0.002 TYR B 481 ARG 0.003 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 91 time to evaluate : 0.846 Fit side-chains REVERT: A 102 LEU cc_start: 0.8146 (mm) cc_final: 0.7864 (mt) REVERT: A 133 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6690 (t80) REVERT: A 368 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5875 (ttt) REVERT: B 102 LEU cc_start: 0.8140 (mm) cc_final: 0.7858 (mt) REVERT: B 133 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6683 (t80) outliers start: 39 outliers final: 28 residues processed: 119 average time/residue: 0.1738 time to fit residues: 30.0176 Evaluate side-chains 119 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8480 Z= 0.181 Angle : 0.686 11.729 11552 Z= 0.336 Chirality : 0.043 0.156 1236 Planarity : 0.005 0.081 1518 Dihedral : 5.553 39.053 1140 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 2.87 % Allowed : 23.68 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -3.45 (0.25), residues: 1034 helix: -1.74 (0.32), residues: 264 sheet: -2.99 (0.45), residues: 106 loop : -2.53 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 570 HIS 0.004 0.001 HIS B 582 PHE 0.010 0.001 PHE A 262 TYR 0.012 0.001 TYR B 418 ARG 0.003 0.000 ARG A 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.925 Fit side-chains REVERT: A 102 LEU cc_start: 0.7976 (mm) cc_final: 0.7680 (mt) REVERT: A 133 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 190 GLU cc_start: 0.7811 (pt0) cc_final: 0.7573 (pt0) REVERT: A 503 GLU cc_start: 0.7097 (pm20) cc_final: 0.6131 (tm-30) REVERT: B 102 LEU cc_start: 0.7973 (mm) cc_final: 0.7680 (mt) REVERT: B 133 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6558 (t80) REVERT: B 190 GLU cc_start: 0.7816 (pt0) cc_final: 0.7577 (pt0) REVERT: B 503 GLU cc_start: 0.7087 (pm20) cc_final: 0.6137 (tm-30) outliers start: 25 outliers final: 21 residues processed: 111 average time/residue: 0.1688 time to fit residues: 27.7045 Evaluate side-chains 107 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.0470 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.201881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.164875 restraints weight = 10877.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.163512 restraints weight = 9218.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.165523 restraints weight = 9701.140| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8480 Z= 0.200 Angle : 0.691 11.310 11552 Z= 0.340 Chirality : 0.044 0.159 1236 Planarity : 0.005 0.085 1518 Dihedral : 5.539 39.056 1140 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 2.87 % Allowed : 23.68 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: -3.37 (0.25), residues: 1034 helix: -1.62 (0.32), residues: 262 sheet: -3.11 (0.45), residues: 110 loop : -2.46 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 570 HIS 0.005 0.001 HIS A 471 PHE 0.017 0.001 PHE B 541 TYR 0.016 0.001 TYR B 147 ARG 0.002 0.000 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1634.83 seconds wall clock time: 30 minutes 44.05 seconds (1844.05 seconds total)