Starting phenix.real_space_refine on Tue Feb 13 14:09:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7met_23803/02_2024/7met_23803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7met_23803/02_2024/7met_23803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7met_23803/02_2024/7met_23803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7met_23803/02_2024/7met_23803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7met_23803/02_2024/7met_23803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7met_23803/02_2024/7met_23803_updated.pdb" } resolution = 3.97 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 ------------------------------------------------------------------------------- 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= 1.000 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 S 20 5.16 5 Cl 2 4.86 5 C 4121 2.51 5 N 1169 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6521 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 3643 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 222} Link IDs: {'PTRANS': 13, 'TRANS': 550} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 799 Unresolved non-hydrogen angles: 1029 Unresolved non-hydrogen dihedrals: 635 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 22, 'ARG:plan': 16, 'TYR:plan': 9, 'ASN:plan1': 14, 'HIS:plan': 9, 'PHE:plan': 7, 'GLU:plan': 15, 'ASP:plan': 19} Unresolved non-hydrogen planarities: 477 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 2834 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PTRANS': 10, 'TRANS': 444} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 756 Unresolved non-hydrogen angles: 972 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 18, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 448 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'Z5G': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.44, per 1000 atoms: 0.68 Number of scatterers: 6521 At special positions: 0 Unit cell: (80.56, 81.62, 136.74, 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) Cl 2 17.00 S 20 16.00 O 1209 8.00 N 1169 7.00 C 4121 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: 2.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 62.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 removed outlier: 3.733A pdb=" N SER A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 51 removed outlier: 3.664A pdb=" N LEU A 23 " --> pdb=" O TRP A 19 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLY A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 102 removed outlier: 4.573A pdb=" N PHE A 61 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Proline residue: A 62 - end of helix removed outlier: 3.634A pdb=" N LEU A 102 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.727A pdb=" N ASN A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 157 Processing helix chain 'A' and resid 167 through 206 Proline residue: A 170 - end of helix removed outlier: 3.973A pdb=" N ASN A 206 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 264 removed outlier: 3.880A pdb=" N SER A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.630A pdb=" N LEU A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 277 through 308 removed outlier: 3.632A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 4.274A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 373 through 381 removed outlier: 4.170A pdb=" N LEU A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 425 through 428 No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 439 through 449 removed outlier: 3.937A pdb=" N ALA A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 508 through 521 removed outlier: 3.687A pdb=" N GLN A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'B' and resid 8 through 52 Proline residue: B 17 - end of helix removed outlier: 4.616A pdb=" N GLY B 20 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 22 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 23 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 25 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 26 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 39 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 46 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 104 Proline residue: B 62 - end of helix removed outlier: 3.677A pdb=" N ARG B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.919A pdb=" N ASP B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 112' Processing helix chain 'B' and resid 115 through 155 removed outlier: 3.623A pdb=" N MET B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 315 removed outlier: 4.105A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 4.697A pdb=" N ASN B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 375 through 382 removed outlier: 4.037A pdb=" N LEU B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 439 through 448 Processing helix chain 'B' and resid 452 through 458 removed outlier: 4.280A pdb=" N LEU B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 554 through 560 Processing helix chain 'B' and resid 562 through 569 removed outlier: 4.151A pdb=" N GLN B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.107A pdb=" N ILE A 493 " --> pdb=" O ALA A 412 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 539 through 542 removed outlier: 3.770A pdb=" N ILE A 540 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 552 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 542 " --> pdb=" O GLU A 550 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU A 550 " --> pdb=" O VAL A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.621A pdb=" N ILE B 335 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 364 through 368 removed outlier: 6.832A pdb=" N ARG B 539 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL B 367 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 541 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 542 " --> pdb=" O GLU B 550 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 550 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 544 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE B 548 " --> pdb=" O ASP B 544 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 411 through 414 removed outlier: 6.385A pdb=" N ILE B 493 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 414 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 495 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR B 523 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU B 496 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 525 " --> pdb=" O LEU B 496 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 342 through 344 removed outlier: 3.605A pdb=" N LEU B 342 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 351 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR B 344 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN B 349 " --> pdb=" O TYR B 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 408 hydrogen bonds defined for protein. 918 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: 1.73 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1129 1.32 - 1.44: 1588 1.44 - 1.56: 3840 1.56 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 6596 Sorted by residual: bond pdb=" C08 Z5G A 601 " pdb=" N10 Z5G A 601 " ideal model delta sigma weight residual 1.345 1.456 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C08 Z5G A 602 " pdb=" N10 Z5G A 602 " ideal model delta sigma weight residual 1.345 1.454 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C11 Z5G A 601 " pdb=" N10 Z5G A 601 " ideal model delta sigma weight residual 1.375 1.454 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C11 Z5G A 602 " pdb=" N10 Z5G A 602 " ideal model delta sigma weight residual 1.375 1.448 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C02 Z5G A 601 " pdb="CL01 Z5G A 601 " ideal model delta sigma weight residual 1.729 1.786 -0.057 2.00e-02 2.50e+03 8.05e+00 ... (remaining 6591 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.57: 48 103.57 - 111.17: 2654 111.17 - 118.78: 2552 118.78 - 126.38: 3733 126.38 - 133.99: 46 Bond angle restraints: 9033 Sorted by residual: angle pdb=" CA PRO B 17 " pdb=" N PRO B 17 " pdb=" CD PRO B 17 " ideal model delta sigma weight residual 112.00 107.68 4.32 1.40e+00 5.10e-01 9.51e+00 angle pdb=" C14 Z5G A 602 " pdb=" C13 Z5G A 602 " pdb=" S12 Z5G A 602 " ideal model delta sigma weight residual 121.23 129.67 -8.44 3.00e+00 1.11e-01 7.91e+00 angle pdb=" C14 Z5G A 601 " pdb=" C13 Z5G A 601 " pdb=" S12 Z5G A 601 " ideal model delta sigma weight residual 121.23 129.50 -8.27 3.00e+00 1.11e-01 7.59e+00 angle pdb=" C MET A 166 " pdb=" N VAL A 167 " pdb=" CA VAL A 167 " ideal model delta sigma weight residual 121.97 126.64 -4.67 1.80e+00 3.09e-01 6.74e+00 angle pdb=" N ILE A 429 " pdb=" CA ILE A 429 " pdb=" C ILE A 429 " ideal model delta sigma weight residual 111.91 109.62 2.29 8.90e-01 1.26e+00 6.63e+00 ... (remaining 9028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 3618 15.90 - 31.81: 204 31.81 - 47.71: 52 47.71 - 63.61: 7 63.61 - 79.51: 7 Dihedral angle restraints: 3888 sinusoidal: 947 harmonic: 2941 Sorted by residual: dihedral pdb=" CA PRO B 17 " pdb=" C PRO B 17 " pdb=" N TYR B 18 " pdb=" CA TYR B 18 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN A 268 " pdb=" C GLN A 268 " pdb=" N ILE A 269 " pdb=" CA ILE A 269 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA VAL A 167 " pdb=" C VAL A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 634 0.027 - 0.053: 304 0.053 - 0.080: 114 0.080 - 0.106: 50 0.106 - 0.133: 30 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CB VAL A 167 " pdb=" CA VAL A 167 " pdb=" CG1 VAL A 167 " pdb=" CG2 VAL A 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CB VAL A 239 " pdb=" CA VAL A 239 " pdb=" CG1 VAL A 239 " pdb=" CG2 VAL A 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA PRO A 106 " pdb=" N PRO A 106 " pdb=" C PRO A 106 " pdb=" CB PRO A 106 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1129 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 16 " 0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 17 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 290 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 291 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 121 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C LYS B 121 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS B 121 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 122 " -0.010 2.00e-02 2.50e+03 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1248 2.77 - 3.30: 6836 3.30 - 3.83: 10485 3.83 - 4.37: 10234 4.37 - 4.90: 18233 Nonbonded interactions: 47036 Sorted by model distance: nonbonded pdb=" OH TYR B 18 " pdb=" OG SER B 89 " model vdw 2.236 2.440 nonbonded pdb=" ND2 ASN B 125 " pdb=" OG SER B 311 " model vdw 2.238 2.520 nonbonded pdb=" O ALA A 132 " pdb=" OG SER A 136 " model vdw 2.285 2.440 nonbonded pdb=" O ALA B 308 " pdb=" OG SER B 311 " model vdw 2.286 2.440 nonbonded pdb=" NE2 GLN A 96 " pdb=" O GLY A 432 " model vdw 2.345 2.520 ... (remaining 47031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.780 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.600 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 0.111 6596 Z= 0.291 Angle : 0.643 8.435 9033 Z= 0.326 Chirality : 0.041 0.133 1132 Planarity : 0.005 0.113 1185 Dihedral : 12.062 79.515 1986 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.24 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1013 helix: 1.90 (0.21), residues: 624 sheet: 1.11 (0.98), residues: 34 loop : -1.27 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 262 HIS 0.002 0.000 HIS A 199 PHE 0.011 0.001 PHE A 71 TYR 0.017 0.001 TYR B 110 ARG 0.015 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8635 (t0) cc_final: 0.8320 (t0) REVERT: A 61 PHE cc_start: 0.8276 (t80) cc_final: 0.8033 (t80) REVERT: A 127 GLU cc_start: 0.7651 (tp30) cc_final: 0.7431 (tp30) REVERT: B 90 LEU cc_start: 0.7958 (tp) cc_final: 0.7676 (tp) REVERT: B 140 ILE cc_start: 0.9026 (tp) cc_final: 0.8824 (tp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1677 time to fit residues: 41.8128 Evaluate side-chains 167 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 50.0000 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 58 optimal weight: 0.0980 chunk 91 optimal weight: 0.1980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6596 Z= 0.318 Angle : 0.675 8.716 9033 Z= 0.373 Chirality : 0.045 0.158 1132 Planarity : 0.007 0.075 1185 Dihedral : 4.656 30.646 1093 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.53 % Favored : 93.88 % Rotamer: Outliers : 3.10 % Allowed : 22.67 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1013 helix: 0.92 (0.20), residues: 633 sheet: 0.71 (0.95), residues: 34 loop : -1.42 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 19 HIS 0.005 0.001 HIS A 199 PHE 0.013 0.002 PHE A 224 TYR 0.016 0.002 TYR B 153 ARG 0.008 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8892 (t0) cc_final: 0.8552 (t0) REVERT: A 127 GLU cc_start: 0.7874 (tp30) cc_final: 0.7552 (tp30) REVERT: A 194 MET cc_start: 0.7733 (tpt) cc_final: 0.7462 (tpt) REVERT: B 13 SER cc_start: 0.8867 (m) cc_final: 0.8127 (t) REVERT: B 47 ILE cc_start: 0.7965 (mm) cc_final: 0.7652 (mm) REVERT: B 90 LEU cc_start: 0.8299 (tp) cc_final: 0.8065 (tp) REVERT: B 121 LYS cc_start: 0.7920 (ttmm) cc_final: 0.7294 (ttmm) outliers start: 13 outliers final: 10 residues processed: 192 average time/residue: 0.1616 time to fit residues: 41.9962 Evaluate side-chains 189 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 40.0000 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 31 optimal weight: 0.0050 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6596 Z= 0.174 Angle : 0.569 8.790 9033 Z= 0.310 Chirality : 0.042 0.158 1132 Planarity : 0.006 0.058 1185 Dihedral : 3.989 26.392 1093 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.54 % Favored : 94.87 % Rotamer: Outliers : 3.34 % Allowed : 25.30 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 1013 helix: 0.83 (0.21), residues: 639 sheet: 0.74 (0.95), residues: 34 loop : -1.27 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 19 HIS 0.002 0.001 HIS A 199 PHE 0.008 0.001 PHE A 214 TYR 0.015 0.001 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8638 (t0) cc_final: 0.8280 (t0) REVERT: A 127 GLU cc_start: 0.7691 (tp30) cc_final: 0.7331 (tp30) REVERT: A 194 MET cc_start: 0.7574 (tpt) cc_final: 0.7309 (tpt) REVERT: B 13 SER cc_start: 0.8907 (m) cc_final: 0.8195 (t) REVERT: B 41 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8355 (mmtt) REVERT: B 90 LEU cc_start: 0.8225 (tp) cc_final: 0.7996 (tp) REVERT: B 123 MET cc_start: 0.8618 (mtp) cc_final: 0.8403 (mtp) outliers start: 14 outliers final: 12 residues processed: 195 average time/residue: 0.1808 time to fit residues: 47.6673 Evaluate side-chains 190 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 0.0060 chunk 26 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6596 Z= 0.228 Angle : 0.595 8.013 9033 Z= 0.323 Chirality : 0.043 0.165 1132 Planarity : 0.005 0.059 1185 Dihedral : 4.164 28.109 1093 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.13 % Favored : 94.27 % Rotamer: Outliers : 5.97 % Allowed : 25.30 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1013 helix: 0.69 (0.21), residues: 634 sheet: 0.65 (0.95), residues: 34 loop : -1.33 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 19 HIS 0.004 0.001 HIS A 199 PHE 0.008 0.001 PHE A 214 TYR 0.016 0.002 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8740 (t0) cc_final: 0.8392 (t0) REVERT: A 127 GLU cc_start: 0.7774 (tp30) cc_final: 0.7441 (tp30) REVERT: A 194 MET cc_start: 0.7912 (tpt) cc_final: 0.7555 (tpt) REVERT: B 13 SER cc_start: 0.8865 (m) cc_final: 0.8152 (t) REVERT: B 72 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7704 (ptp-170) REVERT: B 90 LEU cc_start: 0.8273 (tp) cc_final: 0.8042 (tp) REVERT: B 123 MET cc_start: 0.8599 (mtp) cc_final: 0.8291 (mtp) REVERT: B 127 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7072 (tt0) outliers start: 25 outliers final: 19 residues processed: 191 average time/residue: 0.1595 time to fit residues: 41.7908 Evaluate side-chains 189 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 50.0000 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 83 optimal weight: 40.0000 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 40.0000 chunk 87 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 50.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6596 Z= 0.217 Angle : 0.593 10.598 9033 Z= 0.319 Chirality : 0.043 0.174 1132 Planarity : 0.005 0.059 1185 Dihedral : 4.058 24.679 1093 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.53 % Favored : 93.88 % Rotamer: Outliers : 6.21 % Allowed : 27.68 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1013 helix: 0.71 (0.21), residues: 629 sheet: 0.67 (0.95), residues: 34 loop : -1.32 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.003 0.001 HIS A 199 PHE 0.008 0.001 PHE A 214 TYR 0.015 0.002 TYR B 18 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8767 (t0) cc_final: 0.8429 (t0) REVERT: A 85 VAL cc_start: 0.8598 (m) cc_final: 0.8240 (t) REVERT: A 127 GLU cc_start: 0.7791 (tp30) cc_final: 0.7410 (tp30) REVERT: A 194 MET cc_start: 0.7895 (tpt) cc_final: 0.7638 (tpt) REVERT: B 13 SER cc_start: 0.8891 (m) cc_final: 0.8185 (t) REVERT: B 72 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7920 (ptm160) REVERT: B 90 LEU cc_start: 0.8269 (tp) cc_final: 0.8054 (tp) REVERT: B 123 MET cc_start: 0.8576 (mtp) cc_final: 0.8192 (mtp) REVERT: B 140 ILE cc_start: 0.9071 (tp) cc_final: 0.8865 (tp) REVERT: B 161 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6747 (pt) REVERT: B 287 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8726 (mm) outliers start: 26 outliers final: 21 residues processed: 189 average time/residue: 0.1555 time to fit residues: 39.7641 Evaluate side-chains 199 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 chunk 81 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6596 Z= 0.179 Angle : 0.568 9.644 9033 Z= 0.304 Chirality : 0.042 0.180 1132 Planarity : 0.005 0.059 1185 Dihedral : 3.850 20.712 1093 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.23 % Favored : 94.18 % Rotamer: Outliers : 5.49 % Allowed : 29.83 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 1013 helix: 0.80 (0.21), residues: 638 sheet: 0.75 (0.96), residues: 34 loop : -1.23 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 262 HIS 0.003 0.001 HIS A 199 PHE 0.007 0.001 PHE A 214 TYR 0.013 0.001 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8667 (t0) cc_final: 0.8326 (t0) REVERT: A 85 VAL cc_start: 0.8532 (m) cc_final: 0.8123 (t) REVERT: A 99 TYR cc_start: 0.8313 (t80) cc_final: 0.8108 (t80) REVERT: A 127 GLU cc_start: 0.7695 (tp30) cc_final: 0.7288 (tp30) REVERT: A 194 MET cc_start: 0.7949 (tpt) cc_final: 0.7660 (tpt) REVERT: B 13 SER cc_start: 0.8889 (m) cc_final: 0.8205 (t) REVERT: B 72 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7942 (ptm160) REVERT: B 90 LEU cc_start: 0.8190 (tp) cc_final: 0.7968 (tp) REVERT: B 123 MET cc_start: 0.8558 (mtp) cc_final: 0.8171 (mtp) REVERT: B 287 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8712 (mm) outliers start: 23 outliers final: 21 residues processed: 195 average time/residue: 0.1569 time to fit residues: 42.0652 Evaluate side-chains 194 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 0.0370 chunk 58 optimal weight: 0.9980 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6596 Z= 0.292 Angle : 0.651 10.904 9033 Z= 0.352 Chirality : 0.044 0.179 1132 Planarity : 0.005 0.058 1185 Dihedral : 4.520 23.508 1093 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.22 % Favored : 93.19 % Rotamer: Outliers : 6.68 % Allowed : 33.17 % Favored : 60.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1013 helix: 0.57 (0.21), residues: 626 sheet: 0.50 (0.93), residues: 34 loop : -1.45 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 159 HIS 0.005 0.001 HIS A 199 PHE 0.016 0.002 PHE B 45 TYR 0.018 0.002 TYR A 281 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8873 (t0) cc_final: 0.8537 (t0) REVERT: A 127 GLU cc_start: 0.7857 (tp30) cc_final: 0.7541 (tp30) REVERT: A 194 MET cc_start: 0.7987 (tpt) cc_final: 0.7720 (tpt) REVERT: A 312 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6854 (t) REVERT: B 13 SER cc_start: 0.8932 (m) cc_final: 0.8234 (t) REVERT: B 16 LYS cc_start: 0.8879 (pttp) cc_final: 0.8561 (pttm) REVERT: B 47 ILE cc_start: 0.7661 (mm) cc_final: 0.7164 (mm) REVERT: B 72 ARG cc_start: 0.8358 (ttm170) cc_final: 0.7982 (ptm160) REVERT: B 90 LEU cc_start: 0.8283 (tp) cc_final: 0.8061 (tp) REVERT: B 123 MET cc_start: 0.8381 (mtp) cc_final: 0.7914 (mtp) REVERT: B 140 ILE cc_start: 0.9143 (tp) cc_final: 0.8909 (tp) REVERT: B 161 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6867 (pt) outliers start: 28 outliers final: 22 residues processed: 187 average time/residue: 0.1658 time to fit residues: 41.6637 Evaluate side-chains 196 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6596 Z= 0.219 Angle : 0.608 8.182 9033 Z= 0.327 Chirality : 0.043 0.221 1132 Planarity : 0.005 0.061 1185 Dihedral : 4.296 22.721 1093 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.53 % Favored : 93.88 % Rotamer: Outliers : 7.40 % Allowed : 33.41 % Favored : 59.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 1013 helix: 0.61 (0.21), residues: 633 sheet: 0.54 (0.94), residues: 34 loop : -1.37 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 159 HIS 0.003 0.001 HIS A 199 PHE 0.014 0.001 PHE B 45 TYR 0.017 0.002 TYR A 281 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8767 (t0) cc_final: 0.8420 (t0) REVERT: A 85 VAL cc_start: 0.8533 (m) cc_final: 0.8207 (t) REVERT: A 103 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5513 (pp) REVERT: A 127 GLU cc_start: 0.7807 (tp30) cc_final: 0.7380 (tp30) REVERT: A 194 MET cc_start: 0.7967 (tpt) cc_final: 0.7673 (tpt) REVERT: A 312 VAL cc_start: 0.7076 (OUTLIER) cc_final: 0.6820 (t) REVERT: B 16 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8467 (pttm) REVERT: B 47 ILE cc_start: 0.7631 (mm) cc_final: 0.7254 (mm) REVERT: B 72 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7995 (ptm160) REVERT: B 123 MET cc_start: 0.8375 (mtp) cc_final: 0.7894 (mtp) REVERT: B 140 ILE cc_start: 0.9147 (tp) cc_final: 0.8924 (tp) REVERT: B 287 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8677 (mm) outliers start: 31 outliers final: 24 residues processed: 193 average time/residue: 0.1590 time to fit residues: 41.4000 Evaluate side-chains 203 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.3980 chunk 93 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 40.0000 chunk 85 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6596 Z= 0.205 Angle : 0.621 11.797 9033 Z= 0.325 Chirality : 0.043 0.191 1132 Planarity : 0.005 0.061 1185 Dihedral : 4.171 23.299 1093 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.82 % Favored : 93.58 % Rotamer: Outliers : 7.64 % Allowed : 33.41 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 1013 helix: 0.67 (0.21), residues: 634 sheet: 0.57 (0.94), residues: 34 loop : -1.34 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 159 HIS 0.003 0.001 HIS A 199 PHE 0.013 0.001 PHE B 45 TYR 0.015 0.002 TYR A 14 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8786 (t0) cc_final: 0.8496 (t0) REVERT: A 85 VAL cc_start: 0.8491 (m) cc_final: 0.8107 (t) REVERT: A 103 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5600 (pp) REVERT: A 127 GLU cc_start: 0.7709 (tp30) cc_final: 0.7265 (tp30) REVERT: A 194 MET cc_start: 0.8020 (tpt) cc_final: 0.7713 (tpt) REVERT: A 312 VAL cc_start: 0.7013 (OUTLIER) cc_final: 0.6753 (t) REVERT: B 16 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8421 (pttm) REVERT: B 47 ILE cc_start: 0.7566 (mm) cc_final: 0.7093 (mm) REVERT: B 72 ARG cc_start: 0.8334 (ttm170) cc_final: 0.7970 (ptm160) REVERT: B 101 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8561 (ttpp) REVERT: B 123 MET cc_start: 0.8392 (mtp) cc_final: 0.7890 (mtp) REVERT: B 140 ILE cc_start: 0.9143 (tp) cc_final: 0.8921 (tp) REVERT: B 161 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6809 (pt) REVERT: B 287 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8655 (mm) REVERT: B 315 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8354 (tt) outliers start: 32 outliers final: 25 residues processed: 189 average time/residue: 0.1689 time to fit residues: 42.9155 Evaluate side-chains 203 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 50.0000 chunk 66 optimal weight: 0.0270 chunk 100 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 50.0000 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6596 Z= 0.197 Angle : 0.630 12.754 9033 Z= 0.327 Chirality : 0.043 0.194 1132 Planarity : 0.005 0.061 1185 Dihedral : 4.105 23.053 1093 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.63 % Favored : 93.78 % Rotamer: Outliers : 6.92 % Allowed : 34.84 % Favored : 58.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.27), residues: 1013 helix: 0.69 (0.21), residues: 630 sheet: 0.60 (0.94), residues: 34 loop : -1.36 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS A 199 PHE 0.013 0.001 PHE B 45 TYR 0.017 0.001 TYR A 14 ARG 0.003 0.000 ARG B 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8766 (t0) cc_final: 0.8476 (t0) REVERT: A 85 VAL cc_start: 0.8477 (m) cc_final: 0.8086 (t) REVERT: A 103 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5477 (pp) REVERT: A 127 GLU cc_start: 0.7698 (tp30) cc_final: 0.7234 (tp30) REVERT: A 194 MET cc_start: 0.8000 (tpt) cc_final: 0.7698 (tpt) REVERT: B 16 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8397 (pttm) REVERT: B 47 ILE cc_start: 0.7542 (mm) cc_final: 0.7074 (mm) REVERT: B 72 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7936 (ptm160) REVERT: B 123 MET cc_start: 0.8404 (mtp) cc_final: 0.7908 (mtp) REVERT: B 140 ILE cc_start: 0.9139 (tp) cc_final: 0.8912 (tp) REVERT: B 287 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8626 (mm) REVERT: B 315 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8390 (tt) outliers start: 29 outliers final: 22 residues processed: 185 average time/residue: 0.1690 time to fit residues: 42.3808 Evaluate side-chains 197 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 50.0000 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.214695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.172325 restraints weight = 9594.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.176645 restraints weight = 5735.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.179405 restraints weight = 3881.491| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6596 Z= 0.181 Angle : 0.626 15.224 9033 Z= 0.321 Chirality : 0.043 0.195 1132 Planarity : 0.005 0.062 1185 Dihedral : 3.886 21.215 1093 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.13 % Favored : 94.27 % Rotamer: Outliers : 6.68 % Allowed : 34.37 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 1013 helix: 0.81 (0.21), residues: 629 sheet: 0.69 (0.95), residues: 34 loop : -1.34 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 262 HIS 0.002 0.001 HIS A 199 PHE 0.013 0.001 PHE B 45 TYR 0.017 0.001 TYR A 14 ARG 0.003 0.000 ARG B 304 =============================================================================== Job complete usr+sys time: 1478.83 seconds wall clock time: 27 minutes 36.90 seconds (1656.90 seconds total)