Starting phenix.real_space_refine on Tue Sep 24 21:24:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/09_2024/6jt1_9884.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/09_2024/6jt1_9884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/09_2024/6jt1_9884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/09_2024/6jt1_9884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/09_2024/6jt1_9884.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt1_9884/09_2024/6jt1_9884.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 59 5.16 5 C 5529 2.51 5 N 1462 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8602 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4087 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 4165 Chain: "B" Number of atoms: 4472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 576, 4468 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 576, 4468 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 4553 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU A 147 " occ=0.91 ... (3 atoms not shown) pdb=" CB GLU A 147 " occ=0.91 Time building chain proxies: 9.41, per 1000 atoms: 1.09 Number of scatterers: 8602 At special positions: 0 Unit cell: (148.39, 93.005, 73.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 59 16.00 O 1551 8.00 N 1462 7.00 C 5529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 10 sheets defined 49.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 149 removed outlier: 3.640A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 158 through 174 removed outlier: 4.596A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 228 removed outlier: 4.285A pdb=" N ILE A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.097A pdb=" N HIS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.817A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 334 through 341 removed outlier: 4.038A pdb=" N MET A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.934A pdb=" N THR A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 removed outlier: 4.472A pdb=" N GLY A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 removed outlier: 4.509A pdb=" N LEU A 425 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 removed outlier: 3.930A pdb=" N GLY A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.616A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.800A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 521 Processing helix chain 'A' and resid 544 through 561 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.978A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 removed outlier: 4.193A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 30 removed outlier: 3.673A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 3.929A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.938A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.809A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.734A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 354 removed outlier: 4.183A pdb=" N ASP B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 395 removed outlier: 4.375A pdb=" N TYR B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.579A pdb=" N HIS B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 461 removed outlier: 3.802A pdb=" N LYS B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 removed outlier: 4.012A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.972A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 4.034A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 258 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 232 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.740A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 290 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 482 removed outlier: 5.527A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 removed outlier: 7.611A pdb=" N MET A 573 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASN A 617 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 575 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.739A pdb=" N TYR A 523 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.608A pdb=" N GLN B 178 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.668A pdb=" N ILE B 222 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS B 232 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS B 220 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.890A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 529 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.890A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG B 416 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 530 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP B 418 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 528 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 512 465 hydrogen bonds defined for protein. 1322 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: 2.72 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 3536 1.40 - 1.58: 5154 1.58 - 1.77: 0 1.77 - 1.95: 90 1.95 - 2.13: 4 Bond restraints: 8784 Sorted by residual: bond pdb=" C ASP B 106 " pdb=" O ASP B 106 " ideal model delta sigma weight residual 1.237 1.269 -0.033 1.17e-02 7.31e+03 7.83e+00 bond pdb=" CA THR B 110 " pdb=" C THR B 110 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.30e-02 5.92e+03 5.91e+00 bond pdb=" C ALA B 103 " pdb=" O ALA B 103 " ideal model delta sigma weight residual 1.237 1.263 -0.026 1.17e-02 7.31e+03 5.13e+00 bond pdb=" N THR B 110 " pdb=" CA THR B 110 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.06e+00 bond pdb=" CA ALA B 103 " pdb=" C ALA B 103 " ideal model delta sigma weight residual 1.523 1.549 -0.025 1.30e-02 5.92e+03 3.82e+00 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 11909 4.74 - 9.48: 23 9.48 - 14.22: 1 14.22 - 18.96: 0 18.96 - 23.69: 2 Bond angle restraints: 11935 Sorted by residual: angle pdb=" C THR B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta sigma weight residual 120.56 130.64 -10.08 1.28e+00 6.10e-01 6.20e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C LEU B 108 " pdb=" N ALA B 109 " pdb=" CA ALA B 109 " ideal model delta sigma weight residual 120.28 125.27 -4.99 1.34e+00 5.57e-01 1.39e+01 angle pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CA ALA B 103 " pdb=" C ALA B 103 " pdb=" N LEU B 104 " ideal model delta sigma weight residual 117.30 113.72 3.58 1.16e+00 7.43e-01 9.50e+00 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4901 17.82 - 35.64: 284 35.64 - 53.46: 47 53.46 - 71.28: 17 71.28 - 89.10: 3 Dihedral angle restraints: 5252 sinusoidal: 1996 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER B 209 " pdb=" C SER B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual 180.00 -154.95 -25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASP B 262 " pdb=" C ASP B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 837 0.034 - 0.067: 389 0.067 - 0.101: 116 0.101 - 0.134: 41 0.134 - 0.168: 7 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA HIS B 105 " pdb=" N HIS B 105 " pdb=" C HIS B 105 " pdb=" CB HIS B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ILE B 343 " pdb=" N ILE B 343 " pdb=" C ILE B 343 " pdb=" CB ILE B 343 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 1387 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 112 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 113 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 452 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ASP B 452 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 452 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 453 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 453 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C LEU B 453 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU B 453 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR B 454 " -0.010 2.00e-02 2.50e+03 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 916 2.75 - 3.29: 8595 3.29 - 3.82: 13875 3.82 - 4.36: 15973 4.36 - 4.90: 27325 Nonbonded interactions: 66684 Sorted by model distance: nonbonded pdb=" NH2 ARG A 410 " pdb=" OD1 ASN B 100 " model vdw 2.212 3.120 nonbonded pdb=" O THR B 392 " pdb=" OG SER B 396 " model vdw 2.254 3.040 nonbonded pdb=" O LEU A 74 " pdb=" OG SER A 77 " model vdw 2.274 3.040 nonbonded pdb=" O SER A 581 " pdb=" ND2 ASN A 600 " model vdw 2.290 3.120 nonbonded pdb=" O VAL A 154 " pdb=" N LEU B 340 " model vdw 2.294 3.120 ... (remaining 66679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.630 Find NCS groups from input model: 0.140 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 0.056 8784 Z= 0.252 Angle : 0.770 23.695 11935 Z= 0.392 Chirality : 0.044 0.168 1390 Planarity : 0.004 0.043 1515 Dihedral : 12.201 89.097 3144 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.82 % Favored : 93.82 % Rotamer: Outliers : 4.62 % Allowed : 6.15 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.22), residues: 1101 helix: -1.13 (0.20), residues: 506 sheet: -2.21 (0.31), residues: 212 loop : -2.67 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 22 HIS 0.005 0.001 HIS B 176 PHE 0.025 0.002 PHE A 458 TYR 0.017 0.002 TYR B 454 ARG 0.002 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9258 (mttm) cc_final: 0.9005 (mtmm) REVERT: A 159 LEU cc_start: 0.8786 (pp) cc_final: 0.8431 (tt) REVERT: A 161 ASP cc_start: 0.8632 (m-30) cc_final: 0.8404 (m-30) REVERT: A 209 ARG cc_start: 0.9090 (mtt180) cc_final: 0.8715 (tpt170) REVERT: A 252 TYR cc_start: 0.8984 (p90) cc_final: 0.8368 (p90) REVERT: A 351 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7693 (ptt-90) REVERT: A 364 MET cc_start: 0.8900 (ttp) cc_final: 0.8442 (ttp) REVERT: A 573 MET cc_start: 0.8673 (mmm) cc_final: 0.8303 (tpt) REVERT: A 583 PHE cc_start: 0.9178 (m-80) cc_final: 0.8937 (m-10) REVERT: A 606 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8669 (tppt) REVERT: A 645 ASN cc_start: 0.9225 (m-40) cc_final: 0.8859 (p0) REVERT: A 656 PHE cc_start: 0.8463 (m-80) cc_final: 0.7768 (m-80) REVERT: B 62 ASN cc_start: 0.7387 (m110) cc_final: 0.6870 (t0) REVERT: B 65 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8065 (tp30) REVERT: B 328 MET cc_start: 0.8442 (mtm) cc_final: 0.8208 (mtm) REVERT: B 335 ARG cc_start: 0.8808 (mtt180) cc_final: 0.8434 (mtm-85) REVERT: B 379 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8508 (t) REVERT: B 386 GLU cc_start: 0.9495 (OUTLIER) cc_final: 0.9069 (mp0) REVERT: B 471 LYS cc_start: 0.9182 (tttm) cc_final: 0.8892 (tttp) REVERT: B 569 TYR cc_start: 0.8503 (t80) cc_final: 0.7993 (t80) REVERT: B 571 CYS cc_start: 0.9354 (m) cc_final: 0.9101 (m) REVERT: B 581 GLN cc_start: 0.9383 (mt0) cc_final: 0.8994 (tp-100) REVERT: B 584 LEU cc_start: 0.9638 (mm) cc_final: 0.9418 (mm) outliers start: 42 outliers final: 20 residues processed: 204 average time/residue: 0.1826 time to fit residues: 53.2241 Evaluate side-chains 127 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 201 HIS B 93 ASN B 134 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8784 Z= 0.219 Angle : 0.722 17.307 11935 Z= 0.346 Chirality : 0.044 0.198 1390 Planarity : 0.004 0.044 1515 Dihedral : 7.956 80.633 1241 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.09 % Favored : 95.64 % Rotamer: Outliers : 4.51 % Allowed : 13.08 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.66 (0.23), residues: 1101 helix: -0.08 (0.21), residues: 519 sheet: -1.46 (0.33), residues: 206 loop : -2.20 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.017 0.001 HIS A 100 PHE 0.013 0.002 PHE A 346 TYR 0.019 0.001 TYR B 339 ARG 0.005 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8718 (ttm-80) cc_final: 0.8091 (ptm160) REVERT: A 142 LYS cc_start: 0.9256 (mttm) cc_final: 0.9020 (mtmm) REVERT: A 159 LEU cc_start: 0.8603 (pp) cc_final: 0.8336 (tt) REVERT: A 209 ARG cc_start: 0.9033 (mtt180) cc_final: 0.8692 (tpt170) REVERT: A 281 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8143 (tm) REVERT: A 291 MET cc_start: 0.9444 (ttp) cc_final: 0.9239 (mtm) REVERT: A 351 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7684 (ptm-80) REVERT: A 573 MET cc_start: 0.8704 (mmm) cc_final: 0.8355 (tpt) REVERT: A 583 PHE cc_start: 0.8648 (m-80) cc_final: 0.8437 (m-10) REVERT: A 645 ASN cc_start: 0.9241 (m-40) cc_final: 0.8885 (p0) REVERT: A 656 PHE cc_start: 0.8533 (m-80) cc_final: 0.8316 (m-80) REVERT: B 65 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8198 (tp30) REVERT: B 335 ARG cc_start: 0.8823 (mtt180) cc_final: 0.8465 (mtm-85) REVERT: B 386 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9067 (mp0) REVERT: B 444 MET cc_start: 0.8577 (tmm) cc_final: 0.7948 (mtm) REVERT: B 471 LYS cc_start: 0.9210 (tttm) cc_final: 0.8967 (tttp) REVERT: B 494 ARG cc_start: 0.8655 (ttp-170) cc_final: 0.8381 (ptp-110) REVERT: B 535 GLN cc_start: 0.9021 (pm20) cc_final: 0.8608 (tt0) REVERT: B 569 TYR cc_start: 0.8346 (t80) cc_final: 0.7824 (t80) REVERT: B 571 CYS cc_start: 0.9318 (m) cc_final: 0.9073 (m) REVERT: B 581 GLN cc_start: 0.9382 (mt0) cc_final: 0.9041 (tp-100) REVERT: B 584 LEU cc_start: 0.9636 (mm) cc_final: 0.9398 (mm) REVERT: B 592 MET cc_start: 0.7657 (mtm) cc_final: 0.7258 (mtm) REVERT: B 599 MET cc_start: 0.8225 (ttt) cc_final: 0.7897 (ttt) outliers start: 41 outliers final: 24 residues processed: 160 average time/residue: 0.1889 time to fit residues: 42.9968 Evaluate side-chains 128 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.3980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.194 Angle : 0.703 14.705 11935 Z= 0.330 Chirality : 0.044 0.198 1390 Planarity : 0.004 0.048 1515 Dihedral : 7.218 78.368 1230 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.45 % Favored : 95.27 % Rotamer: Outliers : 4.29 % Allowed : 13.41 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1101 helix: 0.43 (0.22), residues: 521 sheet: -1.14 (0.34), residues: 206 loop : -1.74 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS B 524 PHE 0.017 0.002 PHE B 321 TYR 0.015 0.001 TYR B 339 ARG 0.004 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9235 (mttm) cc_final: 0.9023 (mtmm) REVERT: A 159 LEU cc_start: 0.8547 (pp) cc_final: 0.8239 (tt) REVERT: A 209 ARG cc_start: 0.9035 (mtt180) cc_final: 0.8683 (tpt170) REVERT: A 351 ARG cc_start: 0.7998 (ptm160) cc_final: 0.7620 (ptm-80) REVERT: A 645 ASN cc_start: 0.9248 (m-40) cc_final: 0.8862 (p0) REVERT: A 656 PHE cc_start: 0.8402 (m-80) cc_final: 0.8193 (m-80) REVERT: B 62 ASN cc_start: 0.7422 (m110) cc_final: 0.6975 (t0) REVERT: B 65 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8112 (tp30) REVERT: B 335 ARG cc_start: 0.8843 (mtt180) cc_final: 0.8483 (mtm-85) REVERT: B 347 ASP cc_start: 0.8181 (t0) cc_final: 0.7864 (t0) REVERT: B 386 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.9006 (mp0) REVERT: B 444 MET cc_start: 0.8583 (tmm) cc_final: 0.7944 (mtt) REVERT: B 471 LYS cc_start: 0.9211 (tttm) cc_final: 0.8961 (tttp) REVERT: B 494 ARG cc_start: 0.8707 (ttp-170) cc_final: 0.8349 (ptp-110) REVERT: B 569 TYR cc_start: 0.8274 (t80) cc_final: 0.7652 (t80) REVERT: B 571 CYS cc_start: 0.9228 (m) cc_final: 0.8987 (m) REVERT: B 584 LEU cc_start: 0.9634 (mm) cc_final: 0.9390 (mm) REVERT: B 599 MET cc_start: 0.8235 (ttt) cc_final: 0.7753 (ttt) outliers start: 39 outliers final: 29 residues processed: 154 average time/residue: 0.1734 time to fit residues: 38.7125 Evaluate side-chains 136 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8784 Z= 0.188 Angle : 0.710 14.077 11935 Z= 0.329 Chirality : 0.044 0.257 1390 Planarity : 0.004 0.047 1515 Dihedral : 7.012 79.418 1226 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 4.18 % Allowed : 14.95 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.55 (0.25), residues: 1101 helix: 0.77 (0.22), residues: 520 sheet: -0.97 (0.35), residues: 206 loop : -1.52 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS B 524 PHE 0.017 0.002 PHE A 83 TYR 0.015 0.001 TYR B 339 ARG 0.003 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9225 (mttm) cc_final: 0.9014 (mtmm) REVERT: A 159 LEU cc_start: 0.8549 (pp) cc_final: 0.8338 (tt) REVERT: A 209 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8671 (tpt170) REVERT: A 351 ARG cc_start: 0.7944 (ptm160) cc_final: 0.7565 (ptm-80) REVERT: A 365 ASP cc_start: 0.9153 (p0) cc_final: 0.8662 (p0) REVERT: A 645 ASN cc_start: 0.9248 (m-40) cc_final: 0.8854 (p0) REVERT: B 62 ASN cc_start: 0.7451 (m110) cc_final: 0.7010 (t0) REVERT: B 65 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8227 (tp30) REVERT: B 335 ARG cc_start: 0.8823 (mtt180) cc_final: 0.8497 (mtm-85) REVERT: B 347 ASP cc_start: 0.8024 (t0) cc_final: 0.7703 (t0) REVERT: B 386 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.9027 (mp0) REVERT: B 444 MET cc_start: 0.8556 (tmm) cc_final: 0.7910 (mtt) REVERT: B 458 ASP cc_start: 0.9448 (m-30) cc_final: 0.9246 (m-30) REVERT: B 471 LYS cc_start: 0.9198 (tttm) cc_final: 0.8933 (tttp) REVERT: B 494 ARG cc_start: 0.8736 (ttp-170) cc_final: 0.8340 (ptp-110) REVERT: B 502 ASP cc_start: 0.8801 (m-30) cc_final: 0.8597 (m-30) REVERT: B 569 TYR cc_start: 0.8261 (t80) cc_final: 0.7902 (t80) REVERT: B 571 CYS cc_start: 0.9177 (m) cc_final: 0.8898 (m) REVERT: B 584 LEU cc_start: 0.9628 (mm) cc_final: 0.9387 (mm) REVERT: B 599 MET cc_start: 0.8227 (ttt) cc_final: 0.8009 (ttt) outliers start: 38 outliers final: 30 residues processed: 148 average time/residue: 0.1779 time to fit residues: 38.0196 Evaluate side-chains 136 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.0040 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8784 Z= 0.181 Angle : 0.688 13.555 11935 Z= 0.323 Chirality : 0.043 0.230 1390 Planarity : 0.004 0.060 1515 Dihedral : 6.845 80.262 1226 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 3.96 % Allowed : 15.49 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1101 helix: 1.03 (0.23), residues: 520 sheet: -0.79 (0.35), residues: 206 loop : -1.49 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS B 524 PHE 0.015 0.002 PHE A 83 TYR 0.014 0.001 TYR B 339 ARG 0.003 0.000 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 159 LEU cc_start: 0.8532 (pp) cc_final: 0.8330 (tt) REVERT: A 209 ARG cc_start: 0.9045 (mtt180) cc_final: 0.8663 (tpt170) REVERT: A 351 ARG cc_start: 0.7979 (ptm160) cc_final: 0.7588 (ptm-80) REVERT: A 645 ASN cc_start: 0.9186 (m-40) cc_final: 0.8765 (p0) REVERT: B 62 ASN cc_start: 0.7422 (m110) cc_final: 0.7043 (t0) REVERT: B 65 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8233 (tp30) REVERT: B 163 ASP cc_start: 0.8173 (t0) cc_final: 0.7805 (m-30) REVERT: B 335 ARG cc_start: 0.8819 (mtt180) cc_final: 0.8487 (mtm-85) REVERT: B 347 ASP cc_start: 0.8031 (t0) cc_final: 0.7709 (t0) REVERT: B 386 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.9095 (mp0) REVERT: B 444 MET cc_start: 0.8565 (tmm) cc_final: 0.7937 (mtt) REVERT: B 471 LYS cc_start: 0.9174 (tttm) cc_final: 0.8914 (tttp) REVERT: B 480 MET cc_start: 0.9496 (ttt) cc_final: 0.9293 (tpp) REVERT: B 494 ARG cc_start: 0.8813 (ttp-170) cc_final: 0.8401 (ptp-110) REVERT: B 502 ASP cc_start: 0.8796 (m-30) cc_final: 0.8584 (m-30) REVERT: B 571 CYS cc_start: 0.9190 (m) cc_final: 0.8887 (m) REVERT: B 599 MET cc_start: 0.8192 (ttt) cc_final: 0.7750 (ttt) outliers start: 36 outliers final: 32 residues processed: 141 average time/residue: 0.1952 time to fit residues: 39.4203 Evaluate side-chains 137 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 105 HIS ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8784 Z= 0.205 Angle : 0.690 13.996 11935 Z= 0.323 Chirality : 0.044 0.300 1390 Planarity : 0.004 0.048 1515 Dihedral : 6.712 80.041 1226 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.64 % Favored : 95.18 % Rotamer: Outliers : 3.85 % Allowed : 16.37 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.14 (0.25), residues: 1101 helix: 1.19 (0.23), residues: 516 sheet: -0.76 (0.36), residues: 206 loop : -1.45 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 467 HIS 0.003 0.001 HIS B 524 PHE 0.014 0.002 PHE A 83 TYR 0.022 0.001 TYR B 569 ARG 0.002 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 159 LEU cc_start: 0.8548 (pp) cc_final: 0.8316 (tt) REVERT: A 209 ARG cc_start: 0.9028 (mtt180) cc_final: 0.8648 (tpt170) REVERT: A 573 MET cc_start: 0.8749 (mmm) cc_final: 0.8288 (tpt) REVERT: A 593 ARG cc_start: 0.9280 (mtt-85) cc_final: 0.7855 (ptm-80) REVERT: A 645 ASN cc_start: 0.9170 (m-40) cc_final: 0.8734 (p0) REVERT: B 62 ASN cc_start: 0.7391 (m110) cc_final: 0.7014 (t0) REVERT: B 65 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8224 (tp30) REVERT: B 163 ASP cc_start: 0.8151 (t0) cc_final: 0.7774 (m-30) REVERT: B 335 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8276 (tpp-160) REVERT: B 347 ASP cc_start: 0.8064 (t0) cc_final: 0.7775 (t0) REVERT: B 386 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.9089 (mp0) REVERT: B 444 MET cc_start: 0.8603 (tmm) cc_final: 0.7956 (mtt) REVERT: B 471 LYS cc_start: 0.9165 (tttm) cc_final: 0.8888 (tttp) REVERT: B 494 ARG cc_start: 0.8948 (ttp-170) cc_final: 0.8481 (ptp-110) REVERT: B 502 ASP cc_start: 0.8822 (m-30) cc_final: 0.8578 (m-30) REVERT: B 564 VAL cc_start: 0.9246 (t) cc_final: 0.8942 (m) REVERT: B 571 CYS cc_start: 0.9298 (m) cc_final: 0.8978 (m) outliers start: 35 outliers final: 30 residues processed: 134 average time/residue: 0.1816 time to fit residues: 35.1997 Evaluate side-chains 133 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.0370 chunk 60 optimal weight: 0.0020 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 437 HIS ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8784 Z= 0.163 Angle : 0.699 15.120 11935 Z= 0.321 Chirality : 0.043 0.323 1390 Planarity : 0.004 0.046 1515 Dihedral : 6.587 81.913 1226 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.27 % Favored : 95.55 % Rotamer: Outliers : 3.96 % Allowed : 16.59 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.01 (0.26), residues: 1101 helix: 1.31 (0.23), residues: 513 sheet: -0.61 (0.36), residues: 206 loop : -1.42 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 467 HIS 0.004 0.001 HIS B 524 PHE 0.015 0.002 PHE A 513 TYR 0.016 0.001 TYR A 623 ARG 0.005 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 159 LEU cc_start: 0.8536 (pp) cc_final: 0.8309 (tt) REVERT: A 209 ARG cc_start: 0.9031 (mtt180) cc_final: 0.8641 (tpt170) REVERT: A 556 MET cc_start: 0.9467 (ttm) cc_final: 0.9095 (mmm) REVERT: A 573 MET cc_start: 0.8721 (mmm) cc_final: 0.8292 (tpt) REVERT: A 593 ARG cc_start: 0.9245 (mtt-85) cc_final: 0.7845 (ptm-80) REVERT: A 645 ASN cc_start: 0.9161 (m-40) cc_final: 0.8698 (p0) REVERT: B 62 ASN cc_start: 0.7286 (m110) cc_final: 0.6908 (t0) REVERT: B 65 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8262 (tp30) REVERT: B 163 ASP cc_start: 0.8137 (t0) cc_final: 0.7764 (m-30) REVERT: B 238 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8320 (tmm-80) REVERT: B 335 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8296 (tpp-160) REVERT: B 347 ASP cc_start: 0.8154 (t0) cc_final: 0.7837 (t0) REVERT: B 386 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9064 (mp0) REVERT: B 444 MET cc_start: 0.8585 (tmm) cc_final: 0.7976 (mtt) REVERT: B 471 LYS cc_start: 0.9145 (tttm) cc_final: 0.8877 (tttp) REVERT: B 494 ARG cc_start: 0.8950 (ttp-170) cc_final: 0.8488 (ptp-110) REVERT: B 502 ASP cc_start: 0.8799 (m-30) cc_final: 0.8540 (m-30) REVERT: B 571 CYS cc_start: 0.9291 (m) cc_final: 0.8965 (m) REVERT: B 599 MET cc_start: 0.8673 (ttt) cc_final: 0.8372 (ttt) outliers start: 36 outliers final: 29 residues processed: 138 average time/residue: 0.1933 time to fit residues: 37.5501 Evaluate side-chains 135 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8784 Z= 0.280 Angle : 0.748 17.736 11935 Z= 0.347 Chirality : 0.045 0.335 1390 Planarity : 0.004 0.048 1515 Dihedral : 6.595 78.515 1224 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.82 % Favored : 94.91 % Rotamer: Outliers : 3.52 % Allowed : 17.69 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.05 (0.26), residues: 1101 helix: 1.33 (0.23), residues: 512 sheet: -0.82 (0.36), residues: 207 loop : -1.41 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 467 HIS 0.004 0.001 HIS B 260 PHE 0.031 0.002 PHE A 141 TYR 0.026 0.002 TYR A 623 ARG 0.008 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 159 LEU cc_start: 0.8549 (pp) cc_final: 0.8239 (tt) REVERT: A 209 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8604 (tpt170) REVERT: A 573 MET cc_start: 0.8796 (mmm) cc_final: 0.8298 (tpt) REVERT: A 645 ASN cc_start: 0.9235 (m-40) cc_final: 0.8725 (p0) REVERT: B 62 ASN cc_start: 0.7263 (m110) cc_final: 0.6861 (t0) REVERT: B 65 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8232 (tp30) REVERT: B 163 ASP cc_start: 0.8284 (t0) cc_final: 0.7886 (m-30) REVERT: B 170 ARG cc_start: 0.7715 (ttt90) cc_final: 0.7476 (ttm110) REVERT: B 328 MET cc_start: 0.8326 (mtm) cc_final: 0.7707 (mtm) REVERT: B 335 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8290 (tpp-160) REVERT: B 347 ASP cc_start: 0.8128 (t0) cc_final: 0.7830 (t0) REVERT: B 386 GLU cc_start: 0.9529 (OUTLIER) cc_final: 0.9093 (mp0) REVERT: B 444 MET cc_start: 0.8660 (tmm) cc_final: 0.7986 (mtt) REVERT: B 473 GLU cc_start: 0.8649 (pp20) cc_final: 0.8415 (pp20) REVERT: B 494 ARG cc_start: 0.9010 (ttp-170) cc_final: 0.8713 (tmm-80) REVERT: B 502 ASP cc_start: 0.8837 (m-30) cc_final: 0.8607 (m-30) REVERT: B 571 CYS cc_start: 0.9239 (m) cc_final: 0.8917 (m) REVERT: B 599 MET cc_start: 0.8595 (ttt) cc_final: 0.8313 (ttt) outliers start: 32 outliers final: 28 residues processed: 129 average time/residue: 0.1762 time to fit residues: 33.1935 Evaluate side-chains 131 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 60 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.187 Angle : 0.716 16.108 11935 Z= 0.329 Chirality : 0.044 0.326 1390 Planarity : 0.004 0.046 1515 Dihedral : 6.484 81.492 1222 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.55 % Rotamer: Outliers : 3.19 % Allowed : 18.02 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.05 (0.26), residues: 1101 helix: 1.39 (0.23), residues: 511 sheet: -0.68 (0.36), residues: 207 loop : -1.38 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 602 HIS 0.003 0.001 HIS A 655 PHE 0.035 0.002 PHE A 141 TYR 0.014 0.001 TYR B 339 ARG 0.002 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 159 LEU cc_start: 0.8505 (pp) cc_final: 0.8192 (tt) REVERT: A 209 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8601 (tpt170) REVERT: A 573 MET cc_start: 0.8735 (mmm) cc_final: 0.8275 (tpt) REVERT: A 593 ARG cc_start: 0.9200 (mtt-85) cc_final: 0.7855 (ptm-80) REVERT: A 645 ASN cc_start: 0.9185 (m-40) cc_final: 0.8631 (p0) REVERT: B 62 ASN cc_start: 0.7274 (m110) cc_final: 0.6888 (t0) REVERT: B 65 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8217 (tp30) REVERT: B 163 ASP cc_start: 0.8237 (t0) cc_final: 0.7870 (m-30) REVERT: B 170 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7459 (ttm110) REVERT: B 328 MET cc_start: 0.8309 (mtm) cc_final: 0.7801 (mtm) REVERT: B 335 ARG cc_start: 0.8779 (mtt180) cc_final: 0.8325 (tpp-160) REVERT: B 347 ASP cc_start: 0.8099 (t0) cc_final: 0.7816 (t0) REVERT: B 386 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.9074 (mp0) REVERT: B 444 MET cc_start: 0.8607 (tmm) cc_final: 0.7982 (mtt) REVERT: B 571 CYS cc_start: 0.9222 (m) cc_final: 0.8902 (m) REVERT: B 599 MET cc_start: 0.8577 (ttt) cc_final: 0.8211 (ttt) outliers start: 29 outliers final: 28 residues processed: 129 average time/residue: 0.1913 time to fit residues: 35.1257 Evaluate side-chains 128 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8784 Z= 0.182 Angle : 0.722 15.316 11935 Z= 0.332 Chirality : 0.043 0.327 1390 Planarity : 0.004 0.046 1515 Dihedral : 6.392 81.554 1221 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 3.08 % Allowed : 18.68 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1101 helix: 1.36 (0.23), residues: 513 sheet: -0.60 (0.36), residues: 215 loop : -1.34 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 467 HIS 0.003 0.001 HIS B 492 PHE 0.037 0.002 PHE A 141 TYR 0.035 0.001 TYR A 623 ARG 0.002 0.000 ARG B 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 159 LEU cc_start: 0.8511 (pp) cc_final: 0.8227 (tt) REVERT: A 209 ARG cc_start: 0.8976 (mtt180) cc_final: 0.8593 (tpt170) REVERT: A 573 MET cc_start: 0.8773 (mmm) cc_final: 0.8349 (tpt) REVERT: A 593 ARG cc_start: 0.9187 (mtt-85) cc_final: 0.7803 (ptm-80) REVERT: A 645 ASN cc_start: 0.9169 (m-40) cc_final: 0.8604 (p0) REVERT: B 62 ASN cc_start: 0.7207 (m110) cc_final: 0.6843 (t0) REVERT: B 65 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8185 (tp30) REVERT: B 131 LEU cc_start: 0.7840 (mp) cc_final: 0.7613 (mp) REVERT: B 163 ASP cc_start: 0.8232 (t0) cc_final: 0.7885 (m-30) REVERT: B 170 ARG cc_start: 0.7664 (ttt90) cc_final: 0.7452 (ttm110) REVERT: B 238 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8358 (tmm-80) REVERT: B 310 MET cc_start: 0.9280 (mmt) cc_final: 0.9061 (mmm) REVERT: B 328 MET cc_start: 0.8306 (mtm) cc_final: 0.7795 (mtm) REVERT: B 335 ARG cc_start: 0.8759 (mtt180) cc_final: 0.8344 (tpp-160) REVERT: B 347 ASP cc_start: 0.8214 (t0) cc_final: 0.7912 (t0) REVERT: B 386 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.8933 (mp0) REVERT: B 444 MET cc_start: 0.8611 (tmm) cc_final: 0.7999 (mtt) REVERT: B 494 ARG cc_start: 0.9003 (tmm-80) cc_final: 0.8354 (ptp-110) REVERT: B 535 GLN cc_start: 0.8897 (pm20) cc_final: 0.8593 (tt0) REVERT: B 571 CYS cc_start: 0.9295 (m) cc_final: 0.8980 (m) REVERT: B 599 MET cc_start: 0.8579 (ttt) cc_final: 0.8199 (ttt) outliers start: 28 outliers final: 27 residues processed: 131 average time/residue: 0.1998 time to fit residues: 36.9594 Evaluate side-chains 132 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 548 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 HIS ** 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 = 0.3393 r_free = 0.3393 target = 0.097680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.078982 restraints weight = 20488.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.081122 restraints weight = 12099.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082019 restraints weight = 8429.325| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8784 Z= 0.203 Angle : 0.726 15.773 11935 Z= 0.334 Chirality : 0.044 0.323 1390 Planarity : 0.004 0.046 1515 Dihedral : 6.405 81.252 1221 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.82 % Favored : 95.09 % Rotamer: Outliers : 3.19 % Allowed : 19.01 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1101 helix: 1.33 (0.23), residues: 513 sheet: -0.52 (0.36), residues: 215 loop : -1.30 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 467 HIS 0.003 0.001 HIS B 498 PHE 0.034 0.002 PHE A 141 TYR 0.030 0.001 TYR A 623 ARG 0.002 0.000 ARG B 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.48 seconds wall clock time: 33 minutes 43.76 seconds (2023.76 seconds total)