Starting phenix.real_space_refine on Fri Sep 11 07:51:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jt2_9885/09_2026/6jt2_9885.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jt2_9885/09_2026/6jt2_9885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jt2_9885/09_2026/6jt2_9885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jt2_9885/09_2026/6jt2_9885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jt2_9885/09_2026/6jt2_9885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jt2_9885/09_2026/6jt2_9885.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6jt2_9885/09_2026/6jt2_9885.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jt2_9885/09_2026/6jt2_9885.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 5262 2.51 5 N 1392 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8191 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3742 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 23, 'TRANS': 482} Chain breaks: 8 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 16, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASP:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 4372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 138 Conformer: "B" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 138 bond proxies already assigned to first conformer: 4452 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 Time building chain proxies: 2.76, per 1000 atoms: 0.34 Number of scatterers: 8191 At special positions: 0 Unit cell: (147.345, 87.78, 98.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 56 16.00 P 3 15.00 Mg 2 11.99 O 1475 8.00 N 1392 7.00 C 5262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 446.0 milliseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 50.4% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 149 removed outlier: 3.585A pdb=" N ILE A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.375A pdb=" N VAL A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 155' Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.800A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 4.660A pdb=" N LEU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.643A pdb=" N LYS A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 408 through 458 removed outlier: 4.206A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 4.336A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 removed outlier: 3.508A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.517A pdb=" N GLN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 561 removed outlier: 3.649A pdb=" N GLN A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.642A pdb=" N ASN A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 628 removed outlier: 4.133A pdb=" N ASP A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 18 removed outlier: 4.201A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.931A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.803A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 Processing helix chain 'B' and resid 83 through 90 removed outlier: 3.938A pdb=" N LEU B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 112 removed outlier: 4.732A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.206A pdb=" N ILE B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.692A pdb=" N VAL B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 253' Processing helix chain 'B' and resid 264 through 271 removed outlier: 3.892A pdb=" N SER B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 285 removed outlier: 4.350A pdb=" N LEU B 285 " --> pdb=" O GLU B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.575A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 348 through 398 removed outlier: 4.370A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 408 removed outlier: 4.384A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 443 through 461 Processing helix chain 'B' and resid 491 through 507 removed outlier: 3.532A pdb=" N SER B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.641A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 204 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.563A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525 removed outlier: 4.409A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N MET A 573 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASN A 617 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 575 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 657 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 124 Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.692A pdb=" N GLN B 231 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 277 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 415 through 416 removed outlier: 3.532A pdb=" N GLY B 531 " --> pdb=" O CYS B 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 469 through 474 removed outlier: 7.068A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 474 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN B 563 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 512 461 hydrogen bonds defined for protein. 1326 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: 1.42 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3335 1.39 - 1.56: 4924 1.56 - 1.73: 6 1.73 - 1.90: 86 1.90 - 2.07: 4 Bond restraints: 8355 Sorted by residual: bond pdb=" O3B G2P A1001 " pdb=" PG G2P A1001 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O1A G2P A1001 " pdb=" PA G2P A1001 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O1B G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C4 G2P A1001 " pdb=" C5 G2P A1001 " ideal model delta sigma weight residual 1.384 1.469 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 G2P A1001 " pdb=" C6 G2P A1001 " ideal model delta sigma weight residual 1.420 1.483 -0.063 2.00e-02 2.50e+03 9.79e+00 ... (remaining 8350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 11160 2.27 - 4.54: 170 4.54 - 6.81: 22 6.81 - 9.09: 11 9.09 - 11.36: 4 Bond angle restraints: 11367 Sorted by residual: angle pdb=" PA G2P A1001 " pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 120.83 109.47 11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " pdb=" O3B G2P A1001 " ideal model delta sigma weight residual 99.71 109.82 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C5 G2P A1001 " pdb=" C4 G2P A1001 " pdb=" N3 G2P A1001 " ideal model delta sigma weight residual 128.08 118.69 9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" C TYR B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.28e+00 angle pdb=" C3A G2P A1001 " pdb=" PA G2P A1001 " pdb=" O5' G2P A1001 " ideal model delta sigma weight residual 99.14 108.27 -9.13 3.00e+00 1.11e-01 9.26e+00 ... (remaining 11362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 4662 16.26 - 32.52: 229 32.52 - 48.78: 55 48.78 - 65.03: 14 65.03 - 81.29: 4 Dihedral angle restraints: 4964 sinusoidal: 1841 harmonic: 3123 Sorted by residual: 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 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR B 339 " pdb=" C TYR B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta harmonic sigma weight residual 180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE A 301 " pdb=" C PHE A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1106 0.055 - 0.111: 213 0.111 - 0.166: 22 0.166 - 0.221: 0 0.221 - 0.276: 1 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CB VAL A 462 " pdb=" CA VAL A 462 " pdb=" CG1 VAL A 462 " pdb=" CG2 VAL A 462 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA VAL A 462 " pdb=" N VAL A 462 " pdb=" C VAL A 462 " pdb=" CB VAL A 462 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C2' G2P A1001 " pdb=" C1' G2P A1001 " pdb=" C3' G2P A1001 " pdb=" O2' G2P A1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1339 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 462 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C VAL A 462 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 462 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 463 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 258 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO B 259 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 209 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO B 210 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.031 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 47 2.56 - 3.15: 6531 3.15 - 3.73: 12626 3.73 - 4.32: 16476 4.32 - 4.90: 27806 Nonbonded interactions: 63486 Sorted by model distance: nonbonded pdb=" O2B G2P A1001 " pdb="MG MG A1002 " model vdw 1.980 2.170 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1002 " model vdw 2.095 2.170 nonbonded pdb=" OD2 ASP A 486 " pdb="MG MG A1002 " model vdw 2.101 2.170 nonbonded pdb=" O5' G2P A1001 " pdb="MG MG A1003 " model vdw 2.172 2.170 nonbonded pdb=" O LEU A 520 " pdb=" NE2 GLN A 548 " model vdw 2.259 3.120 ... (remaining 63481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.460 Find NCS groups from input model: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 0.106 8355 Z= 0.217 Angle : 0.738 11.357 11367 Z= 0.377 Chirality : 0.042 0.276 1342 Planarity : 0.005 0.058 1431 Dihedral : 11.139 81.292 2938 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.00 % Favored : 95.71 % Rotamer: Outliers : 3.54 % Allowed : 5.19 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.23), residues: 1049 helix: -1.24 (0.20), residues: 478 sheet: -1.17 (0.35), residues: 192 loop : -2.34 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 552 TYR 0.013 0.001 TYR B 479 PHE 0.016 0.002 PHE A 292 TRP 0.010 0.001 TRP B 602 HIS 0.005 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 ( 8355) covalent geometry : angle 0.73770 / 0.38 (11367) hydrogen bonds : bond 0.13493 / 9.13 ( 461) hydrogen bonds : angle 6.73972 / 4.87 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 CYS cc_start: 0.8998 (t) cc_final: 0.8778 (m) REVERT: A 455 CYS cc_start: 0.8971 (m) cc_final: 0.8406 (t) REVERT: A 479 ASN cc_start: 0.7920 (m110) cc_final: 0.7647 (p0) REVERT: A 514 ASP cc_start: 0.9019 (m-30) cc_final: 0.8740 (m-30) REVERT: A 516 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8498 (mm-40) REVERT: A 543 ASP cc_start: 0.8435 (m-30) cc_final: 0.7491 (p0) REVERT: A 554 VAL cc_start: 0.9375 (t) cc_final: 0.9168 (t) REVERT: A 556 MET cc_start: 0.9443 (tpp) cc_final: 0.8926 (mmm) REVERT: A 583 PHE cc_start: 0.8186 (m-80) cc_final: 0.7859 (m-10) REVERT: B 73 MET cc_start: 0.8564 (tpp) cc_final: 0.8300 (tpp) REVERT: B 106 ASP cc_start: 0.9202 (t0) cc_final: 0.8917 (t0) REVERT: B 119 SER cc_start: 0.9177 (m) cc_final: 0.8363 (p) REVERT: B 160 THR cc_start: 0.8562 (m) cc_final: 0.8351 (p) REVERT: B 211 TYR cc_start: 0.8649 (t80) cc_final: 0.8372 (t80) REVERT: B 228 VAL cc_start: 0.8802 (t) cc_final: 0.8571 (p) REVERT: B 320 LEU cc_start: 0.8545 (tt) cc_final: 0.8089 (tp) REVERT: B 323 CYS cc_start: 0.8540 (p) cc_final: 0.8244 (p) REVERT: B 394 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 491 HIS cc_start: 0.8482 (p90) cc_final: 0.7513 (t-170) REVERT: B 537 MET cc_start: 0.8659 (ttm) cc_final: 0.8425 (ttt) outliers start: 30 outliers final: 11 residues processed: 212 average time/residue: 0.0859 time to fit residues: 25.4157 Evaluate side-chains 123 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0030 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN B 266 HIS B 408 HIS B 548 ASN B 563 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085153 restraints weight = 23462.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087897 restraints weight = 13641.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089836 restraints weight = 9405.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091079 restraints weight = 7271.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091775 restraints weight = 6123.502| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (12 function evaluations) r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8355 Z= 0.135 Angle : 0.686 9.552 11367 Z= 0.342 Chirality : 0.043 0.222 1342 Planarity : 0.005 0.046 1431 Dihedral : 7.346 70.650 1175 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.54 % Allowed : 13.34 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1049 helix: 0.43 (0.22), residues: 487 sheet: -0.91 (0.35), residues: 207 loop : -2.00 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 381 TYR 0.023 0.002 TYR B 237 PHE 0.026 0.002 PHE A 335 TRP 0.033 0.005 TRP A 467 HIS 0.010 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8355) covalent geometry : angle 0.68586 / 0.34 (11367) hydrogen bonds : bond 0.04576 / 3.15 ( 461) hydrogen bonds : angle 4.84024 / 3.50 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6720 (OUTLIER) cc_final: 0.6390 (t80) REVERT: A 455 CYS cc_start: 0.7664 (m) cc_final: 0.7106 (t) REVERT: A 543 ASP cc_start: 0.7489 (m-30) cc_final: 0.6989 (p0) REVERT: A 583 PHE cc_start: 0.8104 (m-80) cc_final: 0.7858 (m-10) REVERT: B 9 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7961 (tt) REVERT: B 69 MET cc_start: 0.7734 (ttm) cc_final: 0.7454 (mtm) REVERT: B 106 ASP cc_start: 0.8594 (t0) cc_final: 0.8199 (t0) REVERT: B 119 SER cc_start: 0.8911 (m) cc_final: 0.7878 (p) REVERT: B 537 MET cc_start: 0.8132 (ttm) cc_final: 0.7831 (ttt) outliers start: 30 outliers final: 18 residues processed: 150 average time/residue: 0.0668 time to fit residues: 15.0008 Evaluate side-chains 127 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 0.0020 chunk 104 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 ASN A 516 GLN B 266 HIS B 346 HIS B 408 HIS B 491 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.105393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083225 restraints weight = 34418.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085154 restraints weight = 21433.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085760 restraints weight = 15793.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088069 restraints weight = 10568.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088234 restraints weight = 7552.611| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (9 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8355 Z= 0.173 Angle : 0.678 8.589 11367 Z= 0.341 Chirality : 0.044 0.275 1342 Planarity : 0.004 0.048 1431 Dihedral : 6.987 68.258 1169 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.49 % Allowed : 14.52 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.25), residues: 1049 helix: 0.85 (0.23), residues: 490 sheet: -0.79 (0.36), residues: 210 loop : -1.87 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 381 TYR 0.015 0.001 TYR B 569 PHE 0.023 0.002 PHE A 141 TRP 0.019 0.003 TRP B 22 HIS 0.011 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 8355) covalent geometry : angle 0.67822 / 0.34 (11367) hydrogen bonds : bond 0.04476 / 3.10 ( 461) hydrogen bonds : angle 4.71367 / 3.40 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6940 (pp) REVERT: A 203 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.6475 (t80) REVERT: A 455 CYS cc_start: 0.7587 (m) cc_final: 0.7181 (t) REVERT: A 543 ASP cc_start: 0.7517 (m-30) cc_final: 0.6931 (p0) REVERT: A 573 MET cc_start: 0.8390 (tpt) cc_final: 0.7975 (tpt) REVERT: B 9 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8153 (tt) REVERT: B 106 ASP cc_start: 0.8736 (t0) cc_final: 0.8280 (t0) REVERT: B 119 SER cc_start: 0.8963 (m) cc_final: 0.7967 (p) REVERT: B 480 MET cc_start: 0.8410 (ttm) cc_final: 0.8206 (ttp) REVERT: B 573 MET cc_start: 0.7433 (mmm) cc_final: 0.7226 (mmm) outliers start: 38 outliers final: 22 residues processed: 140 average time/residue: 0.0613 time to fit residues: 13.2940 Evaluate side-chains 120 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 GLN A 422 GLN A 479 ASN A 516 GLN B 451 ASN B 491 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081727 restraints weight = 23757.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084409 restraints weight = 14005.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086184 restraints weight = 9820.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087503 restraints weight = 7723.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088245 restraints weight = 6535.935| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (10 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8355 Z= 0.138 Angle : 0.622 7.974 11367 Z= 0.308 Chirality : 0.042 0.158 1342 Planarity : 0.004 0.046 1431 Dihedral : 6.539 67.816 1167 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.84 % Allowed : 15.70 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 1049 helix: 1.05 (0.23), residues: 491 sheet: -0.59 (0.36), residues: 210 loop : -1.73 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 381 TYR 0.014 0.001 TYR B 237 PHE 0.020 0.002 PHE A 141 TRP 0.023 0.003 TRP B 22 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8355) covalent geometry : angle 0.62176 / 0.31 (11367) hydrogen bonds : bond 0.04129 / 2.85 ( 461) hydrogen bonds : angle 4.41020 / 3.18 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6811 (pp) REVERT: A 203 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 341 MET cc_start: 0.8017 (tpp) cc_final: 0.7767 (tpt) REVERT: A 479 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6643 (p0) REVERT: A 607 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 9 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8211 (tt) REVERT: B 61 LEU cc_start: 0.8300 (pt) cc_final: 0.7988 (tt) REVERT: B 106 ASP cc_start: 0.8631 (t0) cc_final: 0.8194 (t0) REVERT: B 119 SER cc_start: 0.9168 (m) cc_final: 0.8197 (p) outliers start: 41 outliers final: 26 residues processed: 145 average time/residue: 0.0617 time to fit residues: 13.9093 Evaluate side-chains 128 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN A 479 ASN B 408 HIS B 491 HIS ** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.082621 restraints weight = 34628.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083708 restraints weight = 22889.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084458 restraints weight = 17513.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086830 restraints weight = 11638.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.087075 restraints weight = 8236.945| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8355 Z= 0.140 Angle : 0.630 10.302 11367 Z= 0.309 Chirality : 0.042 0.224 1342 Planarity : 0.004 0.046 1431 Dihedral : 6.367 66.078 1167 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.84 % Allowed : 17.00 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1049 helix: 1.17 (0.23), residues: 494 sheet: -0.38 (0.37), residues: 200 loop : -1.69 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 381 TYR 0.012 0.001 TYR B 479 PHE 0.017 0.002 PHE A 141 TRP 0.020 0.002 TRP B 22 HIS 0.012 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8355) covalent geometry : angle 0.62971 / 0.31 (11367) hydrogen bonds : bond 0.04082 / 2.79 ( 461) hydrogen bonds : angle 4.37349 / 3.16 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6568 (t80) REVERT: A 471 VAL cc_start: 0.7901 (t) cc_final: 0.7647 (m) REVERT: A 607 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7653 (t80) REVERT: B 61 LEU cc_start: 0.8399 (pt) cc_final: 0.8090 (tt) REVERT: B 106 ASP cc_start: 0.8741 (t0) cc_final: 0.8248 (t0) outliers start: 41 outliers final: 31 residues processed: 134 average time/residue: 0.0597 time to fit residues: 12.4209 Evaluate side-chains 130 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 0.0370 chunk 14 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN B 408 HIS B 491 HIS B 563 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083603 restraints weight = 26415.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.086318 restraints weight = 17597.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.086855 restraints weight = 11092.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087129 restraints weight = 8854.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.087602 restraints weight = 8680.247| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8355 Z= 0.111 Angle : 0.605 10.217 11367 Z= 0.295 Chirality : 0.040 0.127 1342 Planarity : 0.004 0.045 1431 Dihedral : 5.935 67.218 1165 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.49 % Allowed : 17.00 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1049 helix: 1.32 (0.23), residues: 491 sheet: -0.31 (0.36), residues: 210 loop : -1.62 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 381 TYR 0.011 0.001 TYR B 479 PHE 0.018 0.002 PHE B 433 TRP 0.022 0.002 TRP B 22 HIS 0.012 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8355) covalent geometry : angle 0.60509 / 0.30 (11367) hydrogen bonds : bond 0.03851 / 2.65 ( 461) hydrogen bonds : angle 4.26869 / 3.09 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8113 (mmm160) REVERT: A 203 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6630 (t80) REVERT: A 573 MET cc_start: 0.8392 (tpt) cc_final: 0.7972 (tpt) REVERT: A 607 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7519 (t80) REVERT: B 61 LEU cc_start: 0.8341 (pt) cc_final: 0.8141 (tt) REVERT: B 106 ASP cc_start: 0.8724 (t0) cc_final: 0.8192 (t0) outliers start: 38 outliers final: 27 residues processed: 134 average time/residue: 0.0595 time to fit residues: 12.4314 Evaluate side-chains 122 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN B 491 HIS B 563 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.081573 restraints weight = 32471.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082516 restraints weight = 21292.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083148 restraints weight = 17760.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.085207 restraints weight = 11405.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085355 restraints weight = 8451.578| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8355 Z= 0.161 Angle : 0.650 10.817 11367 Z= 0.315 Chirality : 0.043 0.352 1342 Planarity : 0.004 0.047 1431 Dihedral : 5.902 63.252 1165 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.19 % Allowed : 16.53 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1049 helix: 1.29 (0.23), residues: 492 sheet: -0.17 (0.37), residues: 210 loop : -1.61 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.012 0.001 TYR B 479 PHE 0.017 0.002 PHE B 433 TRP 0.025 0.003 TRP B 22 HIS 0.008 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 8355) covalent geometry : angle 0.64951 / 0.31 (11367) hydrogen bonds : bond 0.03991 / 2.75 ( 461) hydrogen bonds : angle 4.36378 / 3.15 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6674 (t80) REVERT: A 607 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7678 (t80) REVERT: B 106 ASP cc_start: 0.8703 (t0) cc_final: 0.8139 (t0) outliers start: 44 outliers final: 32 residues processed: 134 average time/residue: 0.0608 time to fit residues: 12.6544 Evaluate side-chains 122 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN B 419 ASN B 563 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081578 restraints weight = 23331.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085810 restraints weight = 17736.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085796 restraints weight = 9344.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085826 restraints weight = 7971.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086208 restraints weight = 7991.311| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8355 Z= 0.147 Angle : 0.642 11.079 11367 Z= 0.311 Chirality : 0.042 0.219 1342 Planarity : 0.004 0.048 1431 Dihedral : 5.935 61.844 1165 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.49 % Allowed : 17.00 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1049 helix: 1.30 (0.23), residues: 493 sheet: -0.17 (0.37), residues: 210 loop : -1.59 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 381 TYR 0.012 0.001 TYR B 479 PHE 0.025 0.002 PHE B 433 TRP 0.027 0.003 TRP B 22 HIS 0.010 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 8355) covalent geometry : angle 0.64222 / 0.31 (11367) hydrogen bonds : bond 0.03961 / 2.73 ( 461) hydrogen bonds : angle 4.36331 / 3.16 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6662 (t80) REVERT: A 607 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7665 (t80) outliers start: 38 outliers final: 32 residues processed: 123 average time/residue: 0.0614 time to fit residues: 11.8366 Evaluate side-chains 123 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.0370 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN B 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.082631 restraints weight = 34411.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084999 restraints weight = 21287.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085545 restraints weight = 14821.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087334 restraints weight = 9870.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087471 restraints weight = 7831.677| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8355 Z= 0.116 Angle : 0.627 11.972 11367 Z= 0.301 Chirality : 0.041 0.198 1342 Planarity : 0.004 0.051 1431 Dihedral : 5.898 63.787 1165 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.37 % Allowed : 17.24 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1049 helix: 1.42 (0.23), residues: 492 sheet: -0.11 (0.37), residues: 210 loop : -1.54 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 381 TYR 0.013 0.001 TYR A 372 PHE 0.025 0.002 PHE B 433 TRP 0.028 0.003 TRP B 22 HIS 0.010 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8355) covalent geometry : angle 0.62673 / 0.30 (11367) hydrogen bonds : bond 0.03825 / 2.64 ( 461) hydrogen bonds : angle 4.28678 / 3.11 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.6590 (t80) REVERT: A 607 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7548 (t80) REVERT: B 503 MET cc_start: 0.8557 (mmm) cc_final: 0.8253 (mmm) outliers start: 37 outliers final: 30 residues processed: 123 average time/residue: 0.0632 time to fit residues: 12.1043 Evaluate side-chains 119 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 97 optimal weight: 0.0050 chunk 100 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082647 restraints weight = 27007.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085652 restraints weight = 17573.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086109 restraints weight = 11270.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086411 restraints weight = 8560.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086788 restraints weight = 8286.464| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8355 Z= 0.118 Angle : 0.630 12.602 11367 Z= 0.303 Chirality : 0.041 0.190 1342 Planarity : 0.004 0.050 1431 Dihedral : 5.859 63.732 1163 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.01 % Allowed : 17.83 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1049 helix: 1.47 (0.23), residues: 492 sheet: -0.03 (0.37), residues: 210 loop : -1.49 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 381 TYR 0.012 0.001 TYR A 372 PHE 0.025 0.002 PHE B 433 TRP 0.049 0.005 TRP B 22 HIS 0.010 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8355) covalent geometry : angle 0.62964 / 0.30 (11367) hydrogen bonds : bond 0.03755 / 2.59 ( 461) hydrogen bonds : angle 4.24867 / 3.09 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.364 Fit side-chains REVERT: A 203 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6631 (t80) REVERT: A 607 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 503 MET cc_start: 0.8618 (mmm) cc_final: 0.8296 (mmm) outliers start: 34 outliers final: 30 residues processed: 121 average time/residue: 0.0640 time to fit residues: 12.1072 Evaluate side-chains 120 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 0.0050 chunk 97 optimal weight: 0.0070 chunk 47 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.081095 restraints weight = 22471.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.083393 restraints weight = 17024.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084099 restraints weight = 10632.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.084406 restraints weight = 9247.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084748 restraints weight = 9002.019| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (8 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8355 Z= 0.171 Angle : 0.659 12.251 11367 Z= 0.321 Chirality : 0.042 0.186 1342 Planarity : 0.004 0.051 1431 Dihedral : 5.875 59.220 1163 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.13 % Allowed : 17.71 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.27), residues: 1049 helix: 1.42 (0.23), residues: 492 sheet: 0.08 (0.38), residues: 208 loop : -1.44 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.012 0.001 TYR B 479 PHE 0.023 0.002 PHE B 433 TRP 0.046 0.004 TRP B 22 HIS 0.010 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8355) covalent geometry : angle 0.65937 / 0.32 (11367) hydrogen bonds : bond 0.03948 / 2.72 ( 461) hydrogen bonds : angle 4.34354 / 3.15 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.53 seconds wall clock time: 26 minutes 28.19 seconds (1588.19 seconds total)