Starting phenix.real_space_refine on Mon Mar 11 15:56:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/03_2024/6jt0_9883_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/03_2024/6jt0_9883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/03_2024/6jt0_9883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/03_2024/6jt0_9883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/03_2024/6jt0_9883_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/03_2024/6jt0_9883_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 Residue "A ARG 95": "NH1" <-> "NH2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8602 Number of models: 1 Model: "" Number of chains: 2 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: 4515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 577, 4511 Unusual residues: {'HEM': 1} Classifications: {'peptide': 576, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552, None: 1} Not linked: pdbres="LYS B 607 " pdbres="HEM B1000 " 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: 577, 4511 Unusual residues: {'HEM': 1} Classifications: {'peptide': 576, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552, None: 1} Not linked: pdbres="LYS B 607 " pdbres="HEM B1000 " 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: 4603 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: 9.23, per 1000 atoms: 1.07 Number of scatterers: 8602 At special positions: 0 Unit cell: (148.39, 96.14, 74.195, 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 - 3.50 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: 3.33 Conformation dependent library (CDL) restraints added in 3.4 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... running ksdssp... Secondary structure from input PDB file: 40 helices and 10 sheets defined 42.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 129 through 148 removed outlier: 3.588A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 159 through 173 removed outlier: 4.595A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 320 through 323 No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 390 through 393 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.471A 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 427 through 457 Processing helix chain 'A' and resid 460 through 468 removed outlier: 3.621A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 499 through 520 Processing helix chain 'A' and resid 545 through 560 Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.773A pdb=" N CYS A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 removed outlier: 3.912A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 Proline residue: B 19 - end of helix removed outlier: 3.931A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 63 through 80 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 94 through 111 removed outlier: 4.871A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.562A pdb=" N THR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 360 through 394 removed outlier: 3.608A pdb=" N LEU B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 440 through 460 removed outlier: 3.709A pdb=" N LYS B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.028A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 Processing helix chain 'B' and resid 566 through 572 Processing sheet with id= A, first strand: chain 'A' and resid 189 through 193 removed outlier: 4.003A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 258 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 232 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.520A pdb=" N PHE A 290 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= D, first strand: chain 'A' and resid 480 through 482 Processing sheet with id= E, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.741A pdb=" N TYR A 523 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 616 through 618 removed outlier: 4.313A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.761A pdb=" N GLN B 178 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 168 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 180 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL B 166 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLU B 182 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N MET B 164 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.613A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP B 224 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.758A pdb=" N VAL B 529 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 479 through 483 removed outlier: 6.462A pdb=" N THR B 525 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1097 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: 2.63 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3085 1.38 - 1.55: 5579 1.55 - 1.71: 26 1.71 - 1.88: 90 1.88 - 2.05: 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 1.266 -0.029 1.17e-02 7.31e+03 6.10e+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 4.90e+00 bond pdb=" CA ALA B 103 " pdb=" C ALA B 103 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.30e-02 5.92e+03 4.74e+00 bond pdb=" CA GLU A 230 " pdb=" CB GLU A 230 " ideal model delta sigma weight residual 1.524 1.551 -0.026 1.22e-02 6.72e+03 4.62e+00 bond pdb=" CA THR B 110 " pdb=" C THR B 110 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.30e-02 5.92e+03 4.59e+00 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 89.05 - 106.50: 265 106.50 - 123.94: 11439 123.94 - 141.39: 229 141.39 - 158.84: 0 158.84 - 176.29: 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 120.56 130.79 -10.23 1.28e+00 6.10e-01 6.38e+01 angle pdb=" N VAL A 231 " pdb=" CA VAL A 231 " pdb=" C VAL A 231 " ideal model delta sigma weight residual 108.17 115.21 -7.04 1.46e+00 4.69e-01 2.33e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C LEU B 108 " pdb=" N ALA B 109 " pdb=" CA ALA B 109 " ideal model delta sigma weight residual 120.28 125.10 -4.82 1.34e+00 5.57e-01 1.29e+01 angle pdb=" N TYR B 395 " pdb=" CA TYR B 395 " pdb=" C TYR B 395 " ideal model delta sigma weight residual 110.06 115.00 -4.94 1.43e+00 4.89e-01 1.19e+01 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4896 17.53 - 35.05: 289 35.05 - 52.58: 48 52.58 - 70.10: 12 70.10 - 87.63: 7 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 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+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 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA HIS A 655 " pdb=" C HIS A 655 " pdb=" N PHE A 656 " pdb=" CA PHE A 656 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1037 0.044 - 0.088: 264 0.088 - 0.132: 82 0.132 - 0.176: 6 0.176 - 0.220: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU B 9 " pdb=" CB LEU B 9 " pdb=" CD1 LEU B 9 " pdb=" CD2 LEU B 9 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 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 2.56 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA VAL B 564 " pdb=" N VAL B 564 " pdb=" C VAL B 564 " pdb=" CB VAL B 564 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1387 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 250 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 251 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 112 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 113 " 0.074 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=" C THR A 328 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 329 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.020 5.00e-02 4.00e+02 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 896 2.75 - 3.29: 8652 3.29 - 3.82: 14007 3.82 - 4.36: 16122 4.36 - 4.90: 27413 Nonbonded interactions: 67090 Sorted by model distance: nonbonded pdb=" O TYR A 623 " pdb=" N LYS A 627 " model vdw 2.212 2.520 nonbonded pdb=" NH2 ARG A 410 " pdb=" OD1 ASN B 100 " model vdw 2.225 2.520 nonbonded pdb=" O THR B 392 " pdb=" OG SER B 396 " model vdw 2.267 2.440 nonbonded pdb=" O SER A 581 " pdb=" ND2 ASN A 600 " model vdw 2.295 2.520 nonbonded pdb=" O LEU A 74 " pdb=" OG SER A 77 " model vdw 2.309 2.440 ... (remaining 67085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.390 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 33.660 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 0.100 8784 Z= 0.238 Angle : 0.710 10.228 11935 Z= 0.391 Chirality : 0.043 0.220 1390 Planarity : 0.004 0.057 1515 Dihedral : 12.208 87.630 3144 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.73 % Favored : 93.91 % Rotamer: Outliers : 4.73 % Allowed : 6.59 % Favored : 88.68 % 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: -2.84 (0.22), residues: 1101 helix: -1.01 (0.20), residues: 505 sheet: -2.10 (0.31), residues: 211 loop : -2.74 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 602 HIS 0.004 0.001 HIS B 176 PHE 0.023 0.002 PHE A 458 TYR 0.016 0.002 TYR B 339 ARG 0.003 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 221 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 178 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9551 (pp) cc_final: 0.9186 (tt) REVERT: A 256 SER cc_start: 0.8985 (t) cc_final: 0.8331 (p) REVERT: A 309 MET cc_start: 0.8928 (ttm) cc_final: 0.8504 (tmm) REVERT: A 341 MET cc_start: 0.9062 (mmt) cc_final: 0.8707 (mmm) REVERT: A 384 SER cc_start: 0.9182 (m) cc_final: 0.8978 (p) REVERT: A 503 ILE cc_start: 0.9734 (mm) cc_final: 0.9468 (tt) REVERT: A 520 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 557 MET cc_start: 0.9490 (mmt) cc_final: 0.9003 (tmm) REVERT: B 65 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9073 (tp30) REVERT: B 69 MET cc_start: 0.9468 (mtm) cc_final: 0.9091 (ptm) REVERT: B 162 ILE cc_start: 0.9430 (pt) cc_final: 0.8938 (mm) REVERT: B 164 MET cc_start: 0.9129 (ttm) cc_final: 0.8891 (ttm) REVERT: B 243 LEU cc_start: 0.8978 (tt) cc_final: 0.8581 (pp) REVERT: B 338 LEU cc_start: 0.9191 (mt) cc_final: 0.8910 (mt) REVERT: B 373 THR cc_start: 0.9292 (m) cc_final: 0.9035 (p) REVERT: B 388 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8615 (tppt) REVERT: B 423 LEU cc_start: 0.9667 (tt) cc_final: 0.9438 (tp) REVERT: B 424 PHE cc_start: 0.9273 (m-80) cc_final: 0.8741 (m-10) REVERT: B 478 LYS cc_start: 0.9289 (mttm) cc_final: 0.8762 (mmtm) REVERT: B 499 LEU cc_start: 0.9494 (tp) cc_final: 0.9061 (tp) REVERT: B 503 MET cc_start: 0.9462 (mtp) cc_final: 0.9098 (mtm) REVERT: B 505 GLU cc_start: 0.9620 (OUTLIER) cc_final: 0.9385 (mt-10) REVERT: B 537 MET cc_start: 0.8906 (mmm) cc_final: 0.8503 (tmm) REVERT: B 541 CYS cc_start: 0.9380 (m) cc_final: 0.8863 (m) REVERT: B 572 LEU cc_start: 0.9692 (mm) cc_final: 0.9441 (mm) REVERT: B 573 MET cc_start: 0.9467 (mmp) cc_final: 0.9226 (mmp) outliers start: 43 outliers final: 11 residues processed: 211 average time/residue: 0.1872 time to fit residues: 55.5646 Evaluate side-chains 116 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 520 LEU 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 379 THR Chi-restraints excluded: chain B residue 505 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 518 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8784 Z= 0.220 Angle : 0.746 14.008 11935 Z= 0.349 Chirality : 0.043 0.203 1390 Planarity : 0.004 0.067 1515 Dihedral : 7.350 80.271 1231 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 3.30 % Allowed : 15.38 % Favored : 81.32 % 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: -1.55 (0.24), residues: 1101 helix: 0.15 (0.22), residues: 504 sheet: -1.48 (0.31), residues: 226 loop : -2.25 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 602 HIS 0.005 0.001 HIS B 498 PHE 0.024 0.002 PHE A 141 TYR 0.023 0.002 TYR B 569 ARG 0.005 0.000 ARG B 464 *********************** 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 136 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9533 (pp) cc_final: 0.9175 (tt) REVERT: A 236 MET cc_start: 0.8313 (mmm) cc_final: 0.8024 (mmm) REVERT: A 256 SER cc_start: 0.9021 (t) cc_final: 0.8479 (p) REVERT: A 384 SER cc_start: 0.9151 (m) cc_final: 0.8901 (p) REVERT: A 483 LEU cc_start: 0.9481 (tp) cc_final: 0.9043 (tt) REVERT: A 520 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8743 (tt) REVERT: A 556 MET cc_start: 0.9743 (ttm) cc_final: 0.9233 (mtt) REVERT: A 557 MET cc_start: 0.9642 (mmt) cc_final: 0.9187 (tpp) REVERT: A 573 MET cc_start: 0.9359 (mmm) cc_final: 0.8618 (mmm) REVERT: B 1 MET cc_start: 0.9264 (tpp) cc_final: 0.8829 (tpp) REVERT: B 11 LEU cc_start: 0.9528 (tp) cc_final: 0.9258 (tp) REVERT: B 69 MET cc_start: 0.9509 (mtm) cc_final: 0.9085 (ptm) REVERT: B 162 ILE cc_start: 0.9485 (pt) cc_final: 0.8929 (mm) REVERT: B 164 MET cc_start: 0.9092 (ttm) cc_final: 0.8619 (ttm) REVERT: B 373 THR cc_start: 0.9349 (m) cc_final: 0.9092 (p) REVERT: B 444 MET cc_start: 0.9310 (tmm) cc_final: 0.8984 (tpt) REVERT: B 503 MET cc_start: 0.9459 (mtp) cc_final: 0.9204 (mtm) REVERT: B 505 GLU cc_start: 0.9600 (OUTLIER) cc_final: 0.9378 (mt-10) REVERT: B 537 MET cc_start: 0.8832 (mmm) cc_final: 0.8583 (tmm) REVERT: B 541 CYS cc_start: 0.9278 (m) cc_final: 0.8858 (m) REVERT: B 572 LEU cc_start: 0.9712 (mm) cc_final: 0.9394 (mm) REVERT: B 573 MET cc_start: 0.9446 (mmp) cc_final: 0.9228 (mmp) outliers start: 30 outliers final: 18 residues processed: 131 average time/residue: 0.1760 time to fit residues: 33.6565 Evaluate side-chains 104 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 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 398 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU 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 393 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN B 367 GLN ** B 563 ASN ** 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: 0.8434 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8784 Z= 0.232 Angle : 0.721 12.959 11935 Z= 0.337 Chirality : 0.043 0.185 1390 Planarity : 0.004 0.052 1515 Dihedral : 6.904 79.237 1230 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.64 % Rotamer: Outliers : 3.96 % Allowed : 15.60 % Favored : 80.44 % 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: -0.76 (0.25), residues: 1101 helix: 0.91 (0.23), residues: 504 sheet: -1.23 (0.32), residues: 226 loop : -1.94 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.003 0.001 HIS A 578 PHE 0.024 0.002 PHE A 141 TYR 0.018 0.002 TYR A 399 ARG 0.003 0.000 ARG A 349 *********************** 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 133 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9549 (pp) cc_final: 0.9215 (tt) REVERT: A 236 MET cc_start: 0.8446 (mmm) cc_final: 0.8078 (mmm) REVERT: A 256 SER cc_start: 0.9156 (t) cc_final: 0.8731 (p) REVERT: A 301 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: A 482 MET cc_start: 0.8864 (tpp) cc_final: 0.8625 (tpp) REVERT: A 483 LEU cc_start: 0.9545 (tp) cc_final: 0.9184 (tt) REVERT: A 520 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8819 (tt) REVERT: A 548 GLN cc_start: 0.9744 (OUTLIER) cc_final: 0.9518 (mp10) REVERT: A 556 MET cc_start: 0.9726 (ttm) cc_final: 0.9233 (mtt) REVERT: A 557 MET cc_start: 0.9654 (mmt) cc_final: 0.9234 (tpp) REVERT: B 11 LEU cc_start: 0.9540 (tp) cc_final: 0.9219 (tp) REVERT: B 164 MET cc_start: 0.8991 (ttm) cc_final: 0.8323 (ttm) REVERT: B 373 THR cc_start: 0.9380 (m) cc_final: 0.9113 (p) REVERT: B 444 MET cc_start: 0.9320 (tmm) cc_final: 0.9053 (tpt) REVERT: B 541 CYS cc_start: 0.9277 (m) cc_final: 0.8855 (m) REVERT: B 548 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.8701 (t0) REVERT: B 572 LEU cc_start: 0.9701 (mm) cc_final: 0.9497 (mm) REVERT: B 573 MET cc_start: 0.9498 (mmp) cc_final: 0.9258 (mmp) REVERT: B 592 MET cc_start: 0.8078 (mmm) cc_final: 0.7552 (mmm) outliers start: 36 outliers final: 24 residues processed: 127 average time/residue: 0.1816 time to fit residues: 33.7330 Evaluate side-chains 116 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 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 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 637 ARG 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 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 553 THR 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: 0.6980 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3078 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= 0.184 Angle : 0.692 13.916 11935 Z= 0.320 Chirality : 0.042 0.165 1390 Planarity : 0.004 0.045 1515 Dihedral : 6.503 77.579 1227 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 3.52 % Allowed : 17.14 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1101 helix: 1.33 (0.24), residues: 503 sheet: -0.84 (0.33), residues: 225 loop : -1.79 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 602 HIS 0.003 0.001 HIS A 578 PHE 0.026 0.002 PHE B 75 TYR 0.016 0.001 TYR A 399 ARG 0.005 0.000 ARG A 420 *********************** 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 131 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9533 (pp) cc_final: 0.9226 (tt) REVERT: A 236 MET cc_start: 0.8471 (mmm) cc_final: 0.8114 (mmm) REVERT: A 256 SER cc_start: 0.9197 (t) cc_final: 0.8776 (p) REVERT: A 341 MET cc_start: 0.9205 (tpp) cc_final: 0.8648 (tpp) REVERT: A 384 SER cc_start: 0.9139 (m) cc_final: 0.8927 (p) REVERT: A 483 LEU cc_start: 0.9578 (tp) cc_final: 0.8860 (tt) REVERT: A 520 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8822 (tt) REVERT: A 548 GLN cc_start: 0.9729 (OUTLIER) cc_final: 0.9498 (pm20) REVERT: A 557 MET cc_start: 0.9659 (mmt) cc_final: 0.9218 (tpp) REVERT: B 1 MET cc_start: 0.9147 (tpp) cc_final: 0.8718 (tpp) REVERT: B 11 LEU cc_start: 0.9545 (tp) cc_final: 0.9185 (tp) REVERT: B 44 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8593 (t0) REVERT: B 164 MET cc_start: 0.9019 (ttm) cc_final: 0.8587 (ttt) REVERT: B 320 LEU cc_start: 0.9569 (tp) cc_final: 0.9261 (tt) REVERT: B 340 LEU cc_start: 0.8545 (tt) cc_final: 0.8119 (tt) REVERT: B 373 THR cc_start: 0.9380 (m) cc_final: 0.9131 (p) REVERT: B 444 MET cc_start: 0.9292 (tmm) cc_final: 0.9088 (tpt) REVERT: B 541 CYS cc_start: 0.9300 (m) cc_final: 0.8863 (m) REVERT: B 548 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8638 (t0) REVERT: B 573 MET cc_start: 0.9456 (mmp) cc_final: 0.9247 (mmp) REVERT: B 592 MET cc_start: 0.7897 (mmm) cc_final: 0.7266 (mmm) outliers start: 32 outliers final: 18 residues processed: 129 average time/residue: 0.1776 time to fit residues: 33.4804 Evaluate side-chains 109 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU 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 409 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 ASP 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 343 ILE Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3365 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= 0.179 Angle : 0.716 14.407 11935 Z= 0.325 Chirality : 0.042 0.200 1390 Planarity : 0.004 0.040 1515 Dihedral : 6.284 75.943 1226 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.41 % Allowed : 18.35 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.46 (0.24), residues: 505 sheet: -0.63 (0.34), residues: 225 loop : -1.64 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 602 HIS 0.002 0.001 HIS B 105 PHE 0.020 0.001 PHE A 141 TYR 0.012 0.001 TYR B 569 ARG 0.003 0.000 ARG B 464 *********************** 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 122 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9517 (pp) cc_final: 0.9209 (tt) REVERT: A 236 MET cc_start: 0.8463 (mmm) cc_final: 0.8137 (mmm) REVERT: A 256 SER cc_start: 0.9255 (t) cc_final: 0.8867 (p) REVERT: A 301 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: A 341 MET cc_start: 0.9238 (tpp) cc_final: 0.8503 (tpp) REVERT: A 548 GLN cc_start: 0.9708 (OUTLIER) cc_final: 0.9476 (pm20) REVERT: A 557 MET cc_start: 0.9616 (mmt) cc_final: 0.9110 (tpp) REVERT: B 1 MET cc_start: 0.9101 (tpp) cc_final: 0.8717 (tpp) REVERT: B 11 LEU cc_start: 0.9562 (tp) cc_final: 0.9209 (tp) REVERT: B 44 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8582 (t0) REVERT: B 320 LEU cc_start: 0.9544 (tp) cc_final: 0.9226 (tt) REVERT: B 373 THR cc_start: 0.9364 (m) cc_final: 0.9140 (p) REVERT: B 478 LYS cc_start: 0.9383 (mttm) cc_final: 0.8841 (mmtm) REVERT: B 541 CYS cc_start: 0.9264 (m) cc_final: 0.8834 (m) REVERT: B 548 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8643 (t0) REVERT: B 592 MET cc_start: 0.7863 (mmm) cc_final: 0.7436 (mmm) outliers start: 31 outliers final: 21 residues processed: 117 average time/residue: 0.1783 time to fit residues: 30.6185 Evaluate side-chains 112 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 51 LEU 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 393 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3584 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= 0.189 Angle : 0.732 13.675 11935 Z= 0.331 Chirality : 0.043 0.270 1390 Planarity : 0.004 0.038 1515 Dihedral : 5.906 75.962 1221 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 3.85 % Allowed : 18.13 % Favored : 78.02 % 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: 0.17 (0.27), residues: 1101 helix: 1.56 (0.24), residues: 504 sheet: -0.38 (0.34), residues: 226 loop : -1.59 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.003 0.001 HIS B 524 PHE 0.020 0.001 PHE A 141 TYR 0.016 0.001 TYR A 399 ARG 0.003 0.000 ARG B 464 *********************** 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 128 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9535 (pp) cc_final: 0.9267 (tp) REVERT: A 236 MET cc_start: 0.8473 (mmm) cc_final: 0.8150 (mmm) REVERT: A 256 SER cc_start: 0.9267 (t) cc_final: 0.8872 (p) REVERT: A 301 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: A 341 MET cc_start: 0.9209 (tpp) cc_final: 0.8477 (tpp) REVERT: A 384 SER cc_start: 0.9127 (m) cc_final: 0.8843 (p) REVERT: A 548 GLN cc_start: 0.9728 (OUTLIER) cc_final: 0.9485 (pm20) REVERT: A 557 MET cc_start: 0.9599 (mmt) cc_final: 0.9120 (tpp) REVERT: A 606 LYS cc_start: 0.9669 (mmtp) cc_final: 0.9440 (mtmt) REVERT: A 626 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9252 (mm) REVERT: B 1 MET cc_start: 0.9142 (tpp) cc_final: 0.8493 (tpp) REVERT: B 11 LEU cc_start: 0.9574 (tp) cc_final: 0.9228 (tp) REVERT: B 44 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8584 (t0) REVERT: B 164 MET cc_start: 0.8914 (ttm) cc_final: 0.8585 (ttt) REVERT: B 320 LEU cc_start: 0.9540 (tp) cc_final: 0.9220 (tt) REVERT: B 373 THR cc_start: 0.9349 (m) cc_final: 0.9129 (p) REVERT: B 478 LYS cc_start: 0.9369 (mttm) cc_final: 0.8957 (mmtm) REVERT: B 541 CYS cc_start: 0.9245 (m) cc_final: 0.8806 (m) REVERT: B 548 ASN cc_start: 0.9201 (OUTLIER) cc_final: 0.8643 (t0) REVERT: B 592 MET cc_start: 0.7783 (mmm) cc_final: 0.7304 (mmm) outliers start: 35 outliers final: 26 residues processed: 123 average time/residue: 0.1788 time to fit residues: 32.4683 Evaluate side-chains 119 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 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 365 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 ASP 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 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 517 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: 0.8980 chunk 60 optimal weight: 0.0870 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3837 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= 0.194 Angle : 0.726 13.572 11935 Z= 0.327 Chirality : 0.043 0.321 1390 Planarity : 0.004 0.038 1515 Dihedral : 5.833 76.508 1221 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.85 % Allowed : 18.79 % Favored : 77.36 % 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: 0.29 (0.27), residues: 1101 helix: 1.58 (0.24), residues: 507 sheet: -0.25 (0.34), residues: 228 loop : -1.47 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.002 0.001 HIS A 578 PHE 0.021 0.001 PHE A 141 TYR 0.017 0.001 TYR B 363 ARG 0.002 0.000 ARG B 464 *********************** 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 123 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9511 (pp) cc_final: 0.9252 (tt) REVERT: A 236 MET cc_start: 0.8616 (mmm) cc_final: 0.8338 (mmm) REVERT: A 256 SER cc_start: 0.9296 (t) cc_final: 0.8855 (p) REVERT: A 301 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: A 341 MET cc_start: 0.9204 (tpp) cc_final: 0.8537 (tpp) REVERT: A 384 SER cc_start: 0.9139 (m) cc_final: 0.8855 (p) REVERT: A 455 CYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9151 (p) REVERT: A 548 GLN cc_start: 0.9716 (OUTLIER) cc_final: 0.9473 (pm20) REVERT: A 556 MET cc_start: 0.9674 (tpp) cc_final: 0.9236 (tpt) REVERT: A 557 MET cc_start: 0.9600 (mmt) cc_final: 0.9319 (tpp) REVERT: A 606 LYS cc_start: 0.9690 (mmtp) cc_final: 0.9475 (mtmt) REVERT: A 626 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9255 (mm) REVERT: B 1 MET cc_start: 0.9148 (tpp) cc_final: 0.8492 (tpp) REVERT: B 11 LEU cc_start: 0.9587 (tp) cc_final: 0.9243 (tp) REVERT: B 44 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8573 (t0) REVERT: B 164 MET cc_start: 0.8874 (ttm) cc_final: 0.8622 (ttt) REVERT: B 320 LEU cc_start: 0.9546 (tp) cc_final: 0.9219 (tt) REVERT: B 373 THR cc_start: 0.9359 (m) cc_final: 0.9145 (p) REVERT: B 444 MET cc_start: 0.9291 (tmm) cc_final: 0.9039 (tpt) REVERT: B 478 LYS cc_start: 0.9407 (mttm) cc_final: 0.8916 (mmtm) REVERT: B 503 MET cc_start: 0.9595 (OUTLIER) cc_final: 0.9284 (mmm) REVERT: B 541 CYS cc_start: 0.9198 (m) cc_final: 0.8775 (m) REVERT: B 548 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8556 (t0) REVERT: B 592 MET cc_start: 0.7667 (mmm) cc_final: 0.7228 (mmm) outliers start: 35 outliers final: 23 residues processed: 117 average time/residue: 0.2086 time to fit residues: 35.5903 Evaluate side-chains 115 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 ASP 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 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 517 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: 0.7980 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4048 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= 0.211 Angle : 0.733 13.123 11935 Z= 0.331 Chirality : 0.043 0.302 1390 Planarity : 0.004 0.037 1515 Dihedral : 5.922 79.289 1221 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.63 % Allowed : 19.12 % Favored : 77.25 % 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: 0.43 (0.27), residues: 1101 helix: 1.55 (0.24), residues: 512 sheet: -0.23 (0.34), residues: 226 loop : -1.17 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.003 0.001 HIS A 578 PHE 0.020 0.001 PHE A 141 TYR 0.017 0.001 TYR B 569 ARG 0.005 0.000 ARG B 552 *********************** 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 121 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9487 (pp) cc_final: 0.9249 (tt) REVERT: A 236 MET cc_start: 0.8608 (mmm) cc_final: 0.8227 (mmm) REVERT: A 256 SER cc_start: 0.9302 (t) cc_final: 0.8940 (p) REVERT: A 301 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: A 341 MET cc_start: 0.9227 (tpp) cc_final: 0.8532 (tpp) REVERT: A 384 SER cc_start: 0.9160 (m) cc_final: 0.8905 (p) REVERT: A 455 CYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9275 (p) REVERT: A 548 GLN cc_start: 0.9721 (OUTLIER) cc_final: 0.9477 (pm20) REVERT: A 557 MET cc_start: 0.9596 (mmt) cc_final: 0.9321 (tpp) REVERT: A 606 LYS cc_start: 0.9694 (mmtp) cc_final: 0.9452 (mtpt) REVERT: A 626 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9276 (mm) REVERT: B 1 MET cc_start: 0.9155 (tpp) cc_final: 0.8472 (tpp) REVERT: B 44 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8532 (t0) REVERT: B 373 THR cc_start: 0.9387 (m) cc_final: 0.9158 (p) REVERT: B 444 MET cc_start: 0.9309 (tmm) cc_final: 0.8984 (tpp) REVERT: B 541 CYS cc_start: 0.9184 (m) cc_final: 0.8758 (m) REVERT: B 548 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8564 (t0) REVERT: B 592 MET cc_start: 0.7951 (mmm) cc_final: 0.7459 (mmm) outliers start: 33 outliers final: 22 residues processed: 113 average time/residue: 0.1801 time to fit residues: 30.0654 Evaluate side-chains 114 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 86 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 344 MET 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 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 ASP 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 393 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 0.0030 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4212 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= 0.178 Angle : 0.745 13.126 11935 Z= 0.331 Chirality : 0.043 0.331 1390 Planarity : 0.003 0.036 1515 Dihedral : 5.596 79.576 1219 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.86 % Allowed : 20.11 % Favored : 77.03 % 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: 0.47 (0.27), residues: 1101 helix: 1.55 (0.24), residues: 513 sheet: -0.07 (0.35), residues: 224 loop : -1.19 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.002 0.001 HIS B 498 PHE 0.020 0.001 PHE A 141 TYR 0.013 0.001 TYR B 569 ARG 0.006 0.000 ARG B 552 *********************** 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 115 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9462 (pp) cc_final: 0.9246 (tt) REVERT: A 236 MET cc_start: 0.8647 (mmm) cc_final: 0.8319 (mmm) REVERT: A 341 MET cc_start: 0.9209 (tpp) cc_final: 0.8580 (tpp) REVERT: A 384 SER cc_start: 0.9121 (m) cc_final: 0.8848 (p) REVERT: A 455 CYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9231 (p) REVERT: A 548 GLN cc_start: 0.9710 (OUTLIER) cc_final: 0.9463 (pm20) REVERT: A 556 MET cc_start: 0.9656 (tpp) cc_final: 0.9450 (tpt) REVERT: A 557 MET cc_start: 0.9576 (mmt) cc_final: 0.9231 (mmm) REVERT: A 606 LYS cc_start: 0.9690 (mmtp) cc_final: 0.9448 (mtpt) REVERT: A 626 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9256 (mm) REVERT: B 1 MET cc_start: 0.9109 (tpp) cc_final: 0.8757 (tpp) REVERT: B 44 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8545 (t0) REVERT: B 73 MET cc_start: 0.9607 (tpp) cc_final: 0.9381 (tpp) REVERT: B 164 MET cc_start: 0.8861 (ttt) cc_final: 0.8401 (ttp) REVERT: B 373 THR cc_start: 0.9380 (m) cc_final: 0.9149 (p) REVERT: B 444 MET cc_start: 0.9297 (tmm) cc_final: 0.9007 (tpp) REVERT: B 478 LYS cc_start: 0.9468 (mttm) cc_final: 0.9027 (mmtm) REVERT: B 503 MET cc_start: 0.9595 (ttm) cc_final: 0.9208 (mmm) REVERT: B 541 CYS cc_start: 0.9188 (m) cc_final: 0.8768 (m) REVERT: B 548 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8545 (t0) REVERT: B 592 MET cc_start: 0.7886 (mmm) cc_final: 0.7404 (mmm) outliers start: 26 outliers final: 18 residues processed: 111 average time/residue: 0.1793 time to fit residues: 29.2657 Evaluate side-chains 110 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 ASP 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 393 LEU Chi-restraints excluded: chain B residue 517 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: 0.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4327 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= 0.184 Angle : 0.754 20.942 11935 Z= 0.330 Chirality : 0.043 0.325 1390 Planarity : 0.004 0.036 1515 Dihedral : 5.595 80.497 1219 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.75 % Allowed : 20.44 % Favored : 76.81 % 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 (0.27), residues: 1101 helix: 1.58 (0.24), residues: 515 sheet: -0.05 (0.35), residues: 226 loop : -1.10 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.002 0.001 HIS B 105 PHE 0.019 0.001 PHE A 141 TYR 0.030 0.001 TYR B 363 ARG 0.006 0.000 ARG B 552 ********************** 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 114 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: 0.9219 (tpp) cc_final: 0.8563 (tpp) REVERT: A 384 SER cc_start: 0.9122 (m) cc_final: 0.8859 (p) REVERT: A 455 CYS cc_start: 0.9471 (OUTLIER) cc_final: 0.9215 (p) REVERT: A 548 GLN cc_start: 0.9710 (OUTLIER) cc_final: 0.9458 (pm20) REVERT: A 557 MET cc_start: 0.9581 (mmt) cc_final: 0.9226 (mmm) REVERT: A 626 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9261 (mm) REVERT: B 1 MET cc_start: 0.9108 (tpp) cc_final: 0.8751 (tpp) REVERT: B 44 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8552 (t0) REVERT: B 73 MET cc_start: 0.9583 (tpp) cc_final: 0.9354 (tpp) REVERT: B 164 MET cc_start: 0.8888 (ttt) cc_final: 0.8477 (ttp) REVERT: B 373 THR cc_start: 0.9385 (m) cc_final: 0.9152 (p) REVERT: B 444 MET cc_start: 0.9298 (tmm) cc_final: 0.9018 (tpp) REVERT: B 503 MET cc_start: 0.9570 (ttm) cc_final: 0.9166 (mmm) REVERT: B 541 CYS cc_start: 0.9161 (m) cc_final: 0.8752 (m) REVERT: B 548 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8525 (t0) REVERT: B 592 MET cc_start: 0.7936 (mmm) cc_final: 0.7416 (mmm) outliers start: 25 outliers final: 20 residues processed: 110 average time/residue: 0.1769 time to fit residues: 28.6830 Evaluate side-chains 109 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 ASP 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 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 517 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: 8.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.044733 restraints weight = 43891.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.046242 restraints weight = 25483.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047299 restraints weight = 17303.320| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8784 Z= 0.315 Angle : 0.781 13.832 11935 Z= 0.360 Chirality : 0.045 0.290 1390 Planarity : 0.004 0.036 1515 Dihedral : 5.940 86.534 1219 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.64 % Allowed : 20.44 % Favored : 76.92 % 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: 0.46 (0.27), residues: 1101 helix: 1.59 (0.24), residues: 507 sheet: -0.15 (0.35), residues: 224 loop : -1.19 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.005 0.001 HIS B 260 PHE 0.025 0.002 PHE A 513 TYR 0.019 0.002 TYR A 399 ARG 0.007 0.000 ARG B 552 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.11 seconds wall clock time: 35 minutes 51.70 seconds (2151.70 seconds total)