Starting phenix.real_space_refine on Thu Feb 13 01:01:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jt2_9885/02_2025/6jt2_9885.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jt2_9885/02_2025/6jt2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6jt2_9885/02_2025/6jt2_9885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jt2_9885/02_2025/6jt2_9885.map" model { file = "/net/cci-nas-00/data/ceres_data/6jt2_9885/02_2025/6jt2_9885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jt2_9885/02_2025/6jt2_9885.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} 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: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} 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: 7.93, per 1000 atoms: 0.97 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.05 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: 3.03 Time building geometry restraints manager: 2.77 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: 4668 16.26 - 32.52: 249 32.52 - 48.78: 56 48.78 - 65.03: 15 65.03 - 81.29: 4 Dihedral angle restraints: 4992 sinusoidal: 1869 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 4989 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: 1.430 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 26.820 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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= 0.283 Angle : 0.738 11.357 11367 Z= 0.377 Chirality : 0.042 0.276 1342 Planarity : 0.005 0.058 1431 Dihedral : 11.363 81.292 2966 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (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 TRP 0.010 0.001 TRP B 602 HIS 0.005 0.001 HIS B 105 PHE 0.016 0.002 PHE A 292 TYR 0.013 0.001 TYR B 479 ARG 0.003 0.000 ARG B 552 *********************** 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 : 0.908 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: 0.2000 time to fit residues: 58.2046 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 : 0.942 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 96 optimal weight: 10.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 408 HIS B 548 ASN B 563 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.107866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086564 restraints weight = 25649.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087366 restraints weight = 15938.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088352 restraints weight = 12808.879| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8355 Z= 0.205 Angle : 0.695 10.251 11367 Z= 0.348 Chirality : 0.043 0.191 1342 Planarity : 0.005 0.047 1431 Dihedral : 7.828 69.584 1203 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.01 % Allowed : 12.63 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1049 helix: 0.43 (0.22), residues: 487 sheet: -0.91 (0.35), residues: 207 loop : -2.00 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 467 HIS 0.010 0.001 HIS B 266 PHE 0.024 0.002 PHE A 335 TYR 0.025 0.002 TYR B 237 ARG 0.008 0.001 ARG B 381 *********************** 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 154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6449 (t80) REVERT: A 455 CYS cc_start: 0.7750 (m) cc_final: 0.7201 (t) REVERT: A 511 THR cc_start: 0.9177 (p) cc_final: 0.8973 (t) REVERT: A 543 ASP cc_start: 0.7737 (m-30) cc_final: 0.7104 (p0) REVERT: A 583 PHE cc_start: 0.8135 (m-80) cc_final: 0.7927 (m-10) REVERT: B 106 ASP cc_start: 0.8677 (t0) cc_final: 0.8269 (t0) REVERT: B 119 SER cc_start: 0.8914 (m) cc_final: 0.7887 (p) REVERT: B 491 HIS cc_start: 0.7415 (p90) cc_final: 0.7183 (t-170) REVERT: B 537 MET cc_start: 0.8305 (ttm) cc_final: 0.8019 (ttt) outliers start: 34 outliers final: 21 residues processed: 144 average time/residue: 0.1696 time to fit residues: 35.7153 Evaluate side-chains 124 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 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 616 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 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 98 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN B 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.079371 restraints weight = 19174.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081628 restraints weight = 12243.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083162 restraints weight = 9026.128| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 8355 Z= 0.371 Angle : 0.734 9.091 11367 Z= 0.372 Chirality : 0.046 0.271 1342 Planarity : 0.005 0.050 1431 Dihedral : 7.656 65.021 1198 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.37 % Allowed : 14.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.26), residues: 1049 helix: 0.77 (0.23), residues: 493 sheet: -0.76 (0.36), residues: 210 loop : -1.85 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 22 HIS 0.019 0.002 HIS B 266 PHE 0.026 0.002 PHE A 458 TYR 0.018 0.002 TYR B 569 ARG 0.005 0.001 ARG B 381 *********************** 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 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7057 (pp) REVERT: A 203 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6447 (t80) REVERT: A 399 TYR cc_start: 0.7146 (m-80) cc_final: 0.6827 (m-10) REVERT: A 455 CYS cc_start: 0.7611 (m) cc_final: 0.7254 (t) REVERT: B 1 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8002 (ttp) REVERT: B 9 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8223 (tt) REVERT: B 106 ASP cc_start: 0.8640 (t0) cc_final: 0.8147 (t0) REVERT: B 119 SER cc_start: 0.9134 (m) cc_final: 0.8255 (p) REVERT: B 491 HIS cc_start: 0.7472 (p90) cc_final: 0.7221 (t-170) outliers start: 37 outliers final: 22 residues processed: 133 average time/residue: 0.1547 time to fit residues: 31.1138 Evaluate side-chains 116 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 348 VAL 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 559 LEU 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 9 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 422 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 87 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 422 GLN A 479 ASN B 451 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079851 restraints weight = 23353.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.082467 restraints weight = 13850.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084275 restraints weight = 9731.138| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 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 = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8355 Z= 0.234 Angle : 0.632 8.258 11367 Z= 0.316 Chirality : 0.043 0.159 1342 Planarity : 0.004 0.047 1431 Dihedral : 7.265 64.197 1196 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.72 % Allowed : 15.35 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1049 helix: 1.13 (0.23), residues: 490 sheet: -0.65 (0.36), residues: 210 loop : -1.74 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 22 HIS 0.004 0.001 HIS A 545 PHE 0.022 0.002 PHE A 458 TYR 0.016 0.001 TYR B 237 ARG 0.004 0.000 ARG B 381 *********************** 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 141 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7045 (pp) REVERT: A 203 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 341 MET cc_start: 0.8138 (tpp) cc_final: 0.7826 (tpt) REVERT: A 399 TYR cc_start: 0.7220 (m-80) cc_final: 0.6959 (m-80) REVERT: A 471 VAL cc_start: 0.7982 (t) cc_final: 0.7767 (m) REVERT: A 607 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7718 (t80) REVERT: B 61 LEU cc_start: 0.8376 (pt) cc_final: 0.8065 (tt) REVERT: B 106 ASP cc_start: 0.8596 (t0) cc_final: 0.8067 (t0) REVERT: B 119 SER cc_start: 0.9150 (m) cc_final: 0.8268 (p) REVERT: B 328 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7973 (mmm) REVERT: B 491 HIS cc_start: 0.7487 (p90) cc_final: 0.7175 (t-170) REVERT: B 592 MET cc_start: 0.7496 (ppp) cc_final: 0.7240 (ppp) outliers start: 40 outliers final: 26 residues processed: 136 average time/residue: 0.1556 time to fit residues: 32.1729 Evaluate side-chains 125 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR 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 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 478 SER 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 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 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 328 MET 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 14 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 0.0270 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.103046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.080202 restraints weight = 41559.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081921 restraints weight = 26212.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.082511 restraints weight = 18735.594| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3625 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= 0.249 Angle : 0.625 8.285 11367 Z= 0.312 Chirality : 0.042 0.166 1342 Planarity : 0.004 0.046 1431 Dihedral : 6.735 62.448 1194 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.84 % Allowed : 15.11 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1049 helix: 1.23 (0.23), residues: 493 sheet: -0.53 (0.36), residues: 210 loop : -1.76 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 22 HIS 0.004 0.001 HIS A 406 PHE 0.019 0.002 PHE A 458 TYR 0.012 0.001 TYR B 479 ARG 0.004 0.000 ARG B 381 *********************** 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 141 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.7016 (pp) REVERT: A 203 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6595 (t80) REVERT: A 399 TYR cc_start: 0.7374 (m-80) cc_final: 0.7039 (m-80) REVERT: A 514 ASP cc_start: 0.8513 (m-30) cc_final: 0.8245 (m-30) REVERT: A 607 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7837 (t80) REVERT: B 61 LEU cc_start: 0.8445 (pt) cc_final: 0.8152 (tt) REVERT: B 106 ASP cc_start: 0.8692 (t0) cc_final: 0.8118 (t0) REVERT: B 119 SER cc_start: 0.9077 (m) cc_final: 0.8190 (p) REVERT: B 338 LEU cc_start: 0.9067 (mt) cc_final: 0.8770 (mt) outliers start: 41 outliers final: 29 residues processed: 134 average time/residue: 0.1420 time to fit residues: 28.8204 Evaluate side-chains 127 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR 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 380 LEU Chi-restraints excluded: chain A residue 422 GLN 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 525 VAL Chi-restraints excluded: chain A residue 527 THR 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 256 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 528 VAL 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 51 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.104805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082451 restraints weight = 34591.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.083149 restraints weight = 22448.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.083960 restraints weight = 17249.541| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 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 = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8355 Z= 0.193 Angle : 0.609 10.426 11367 Z= 0.301 Chirality : 0.041 0.285 1342 Planarity : 0.004 0.045 1431 Dihedral : 6.571 62.964 1194 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.37 % Allowed : 15.82 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1049 helix: 1.40 (0.23), residues: 490 sheet: -0.36 (0.36), residues: 210 loop : -1.64 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 22 HIS 0.004 0.001 HIS A 406 PHE 0.016 0.002 PHE A 458 TYR 0.012 0.001 TYR B 479 ARG 0.003 0.000 ARG B 381 *********************** 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 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.6661 (t80) REVERT: A 573 MET cc_start: 0.8467 (tpt) cc_final: 0.7996 (tpt) REVERT: A 607 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7850 (t80) REVERT: B 61 LEU cc_start: 0.8420 (pt) cc_final: 0.8142 (tt) REVERT: B 106 ASP cc_start: 0.8672 (t0) cc_final: 0.8115 (t0) REVERT: B 501 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8479 (mm) outliers start: 37 outliers final: 28 residues processed: 133 average time/residue: 0.1550 time to fit residues: 30.8668 Evaluate side-chains 124 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR 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 380 LEU Chi-restraints excluded: chain A residue 422 GLN 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 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 164 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 256 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 501 LEU Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 419 ASN ** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080698 restraints weight = 18647.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083037 restraints weight = 11814.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084699 restraints weight = 8604.610| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 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 = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8355 Z= 0.201 Angle : 0.604 10.410 11367 Z= 0.299 Chirality : 0.041 0.208 1342 Planarity : 0.004 0.045 1431 Dihedral : 6.466 62.106 1194 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.37 % Allowed : 16.77 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1049 helix: 1.43 (0.23), residues: 491 sheet: -0.24 (0.37), residues: 210 loop : -1.60 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 22 HIS 0.012 0.001 HIS B 498 PHE 0.016 0.002 PHE A 458 TYR 0.012 0.001 TYR B 479 ARG 0.003 0.000 ARG B 381 *********************** 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 127 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6587 (t80) REVERT: A 399 TYR cc_start: 0.7493 (m-80) cc_final: 0.7066 (m-10) REVERT: A 607 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7767 (t80) REVERT: B 61 LEU cc_start: 0.8368 (pt) cc_final: 0.8124 (tt) REVERT: B 501 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8480 (mm) outliers start: 37 outliers final: 30 residues processed: 122 average time/residue: 0.1663 time to fit residues: 30.8513 Evaluate side-chains 121 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 422 GLN 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 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 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 256 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 501 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 516 GLN 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 = 0.3513 r_free = 0.3513 target = 0.102824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.080180 restraints weight = 32014.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.082208 restraints weight = 20911.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.082779 restraints weight = 15110.465| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8355 Z= 0.293 Angle : 0.641 11.279 11367 Z= 0.318 Chirality : 0.042 0.195 1342 Planarity : 0.004 0.046 1431 Dihedral : 6.460 58.507 1193 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.84 % Allowed : 16.17 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1049 helix: 1.36 (0.23), residues: 493 sheet: -0.11 (0.38), residues: 210 loop : -1.55 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 22 HIS 0.011 0.001 HIS B 498 PHE 0.019 0.002 PHE A 458 TYR 0.015 0.001 TYR A 372 ARG 0.003 0.000 ARG B 381 *********************** 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 129 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8161 (mmm160) REVERT: A 203 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6696 (t80) REVERT: A 607 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7910 (t80) REVERT: B 61 LEU cc_start: 0.8411 (pt) cc_final: 0.8162 (tt) REVERT: B 501 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8491 (mm) outliers start: 41 outliers final: 33 residues processed: 123 average time/residue: 0.1528 time to fit residues: 28.6387 Evaluate side-chains 123 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 525 VAL 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 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 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 256 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 501 LEU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 92 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082812 restraints weight = 31803.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084503 restraints weight = 18915.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084982 restraints weight = 15466.173| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 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 = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8355 Z= 0.167 Angle : 0.624 12.158 11367 Z= 0.303 Chirality : 0.041 0.294 1342 Planarity : 0.004 0.044 1431 Dihedral : 6.429 62.095 1193 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.25 % Allowed : 17.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 1049 helix: 1.48 (0.23), residues: 493 sheet: 0.02 (0.38), residues: 208 loop : -1.53 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 22 HIS 0.011 0.001 HIS B 498 PHE 0.016 0.001 PHE B 457 TYR 0.016 0.001 TYR A 372 ARG 0.003 0.000 ARG B 381 *********************** 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 126 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8105 (mmm160) REVERT: A 203 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6649 (t80) REVERT: A 399 TYR cc_start: 0.7666 (m-80) cc_final: 0.7303 (m-10) REVERT: A 607 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7730 (t80) REVERT: B 61 LEU cc_start: 0.8365 (pt) cc_final: 0.8136 (tt) REVERT: B 501 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (mm) REVERT: B 503 MET cc_start: 0.8651 (mmm) cc_final: 0.8411 (mmm) outliers start: 36 outliers final: 28 residues processed: 120 average time/residue: 0.1617 time to fit residues: 29.1984 Evaluate side-chains 119 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR 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 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 502 VAL Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 559 LEU 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 80 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET 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 501 LEU Chi-restraints excluded: chain B residue 528 VAL 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 100 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 25 optimal weight: 0.0010 chunk 19 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 overall best weight: 0.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3564 r_free = 0.3564 target = 0.106231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084697 restraints weight = 22031.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084930 restraints weight = 13458.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085844 restraints weight = 12382.053| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 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 = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8355 Z= 0.159 Angle : 0.615 12.253 11367 Z= 0.295 Chirality : 0.041 0.281 1342 Planarity : 0.004 0.049 1431 Dihedral : 6.297 63.558 1193 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.01 % Allowed : 17.36 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 1049 helix: 1.56 (0.23), residues: 493 sheet: 0.11 (0.38), residues: 208 loop : -1.51 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 22 HIS 0.011 0.001 HIS B 498 PHE 0.016 0.001 PHE B 321 TYR 0.018 0.001 TYR A 372 ARG 0.003 0.000 ARG B 381 ********************** 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 132 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8351 (mmm160) cc_final: 0.8027 (mmm160) REVERT: A 203 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6565 (t80) REVERT: A 399 TYR cc_start: 0.7504 (m-80) cc_final: 0.7190 (m-10) REVERT: A 607 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 626 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (mm) REVERT: B 501 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8491 (mm) outliers start: 34 outliers final: 24 residues processed: 125 average time/residue: 0.1705 time to fit residues: 32.5919 Evaluate side-chains 116 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 422 GLN 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 533 CYS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 80 GLU 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 501 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0070 chunk 96 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 0.0060 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS B 563 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.106337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.085146 restraints weight = 22435.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.084212 restraints weight = 14716.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084865 restraints weight = 13032.804| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 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 = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.267 8355 Z= 0.269 Angle : 1.130 59.200 11367 Z= 0.685 Chirality : 0.055 1.152 1342 Planarity : 0.005 0.106 1431 Dihedral : 6.480 63.573 1193 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.54 % Allowed : 17.95 % Favored : 78.51 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 1049 helix: 1.52 (0.23), residues: 493 sheet: 0.10 (0.38), residues: 208 loop : -1.51 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 22 HIS 0.011 0.001 HIS B 498 PHE 0.015 0.002 PHE B 321 TYR 0.015 0.001 TYR A 372 ARG 0.003 0.000 ARG B 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2830.18 seconds wall clock time: 51 minutes 29.07 seconds (3089.07 seconds total)