Starting phenix.real_space_refine on Fri Sep 11 02:08:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5tv4_8469/09_2026/5tv4_8469.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tv4_8469/09_2026/5tv4_8469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5tv4_8469/09_2026/5tv4_8469.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5tv4_8469/09_2026/5tv4_8469.cif" model { file = "/net/cci-nas-00/data/ceres_data/5tv4_8469/09_2026/5tv4_8469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tv4_8469/09_2026/5tv4_8469.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5tv4_8469/09_2026/5tv4_8469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tv4_8469/09_2026/5tv4_8469.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 16 5.16 5 C 4040 2.51 5 N 1234 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6548 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3205 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 375} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 555} Unresolved chain links: 1 Unresolved chain link angles: 11 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1255 Unresolved non-hydrogen angles: 1592 Unresolved non-hydrogen dihedrals: 1004 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 17, 'PHE:plan': 13, 'ARG:plan': 29, 'ASN:plan1': 19, 'ASP:plan': 26, 'TYR:plan': 11, 'GLU:plan': 28, 'TRP:plan': 1, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 654 Chain: "B" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3180 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 555} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1279 Unresolved non-hydrogen angles: 1619 Unresolved non-hydrogen dihedrals: 1021 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 17, 'PHE:plan': 16, 'ARG:plan': 28, 'ASP:plan': 26, 'GLU:plan': 28, 'TYR:plan': 8, 'TRP:plan': 1, 'ASN:plan1': 17, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 640 Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 91 Unusual residues: {'GMH': 3, 'KDO': 2, 'PA1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {'PO4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 60 Unusual residues: {'DAO': 1, 'FTT': 4, 'MYR': 1, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'FTT:plan-1': 4, 'MYR:plan-1': 1, 'DAO:plan-1': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 1.48, per 1000 atoms: 0.23 Number of scatterers: 6548 At special positions: 0 Unit cell: (91.02, 84.87, 134.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 4 15.00 O 1254 8.00 N 1234 7.00 C 4040 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=7, symmetry=0 Links applied ?1-6 " PA1 C 1 " - " PA1 C 2 " ?2-4 " KDO C 3 " - " KDO C 7 " ?2-6 " PA1 C 2 " - " KDO C 3 " ALPHA1-3 " GMH C 4 " - " GMH C 5 " ALPHA1-5 " KDO C 3 " - " GMH C 4 " ALPHA1-7 " GMH C 5 " - " GMH C 6 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 438.6 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 69.4% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 24 through 48 Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 66 through 110 removed outlier: 3.754A pdb=" N VAL A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 120 through 148 removed outlier: 3.736A pdb=" N ALA A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.642A pdb=" N ILE A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'A' and resid 174 through 193 Processing helix chain 'A' and resid 195 through 213 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 222 through 251 removed outlier: 3.894A pdb=" N LYS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.820A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 323 removed outlier: 3.619A pdb=" N ILE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.091A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.993A pdb=" N LEU A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.817A pdb=" N ILE A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 5.689A pdb=" N ARG A 441 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 443 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 482 through 497 Processing helix chain 'A' and resid 512 through 528 Processing helix chain 'A' and resid 538 through 545 Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.521A pdb=" N LEU A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.059A pdb=" N TRP B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 24 through 49 removed outlier: 3.799A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 55 Processing helix chain 'B' and resid 60 through 109 removed outlier: 3.728A pdb=" N LEU B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 120 through 162 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'B' and resid 174 through 213 removed outlier: 3.979A pdb=" N VAL B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 222 through 251 removed outlier: 3.706A pdb=" N PHE B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 removed outlier: 4.102A pdb=" N LEU B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Proline residue: B 273 - end of helix removed outlier: 3.549A pdb=" N MET B 276 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.952A pdb=" N ILE B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 Proline residue: B 297 - end of helix removed outlier: 3.764A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 323 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.693A pdb=" N SER B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 446 through 456 removed outlier: 4.510A pdb=" N ILE B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 512 through 527 Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.921A pdb=" N LYS B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 545 " --> pdb=" O THR B 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 561 through 567 removed outlier: 3.904A pdb=" N GLU B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 579 removed outlier: 4.202A pdb=" N GLN B 574 " --> pdb=" O GLY B 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 367 removed outlier: 5.316A pdb=" N VAL A 347 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASN A 363 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG A 345 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS A 365 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU A 343 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP A 341 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL A 347 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU A 397 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 374 removed outlier: 6.407A pdb=" N VAL A 372 " --> pdb=" O VAL A 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 552 removed outlier: 6.773A pdb=" N VAL A 550 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 344 through 347 removed outlier: 4.942A pdb=" N ARG B 345 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 364 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 421 removed outlier: 6.905A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 536 hydrogen bonds defined for protein. 1572 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: 0.82 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2305 1.34 - 1.46: 775 1.46 - 1.57: 3475 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 6586 Sorted by residual: bond pdb=" C5 PA1 C 2 " pdb=" O5 PA1 C 2 " ideal model delta sigma weight residual 1.417 1.533 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" O3 PO4 A 608 " pdb=" P PO4 A 608 " ideal model delta sigma weight residual 1.569 1.464 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" O3 PO4 A 610 " pdb=" P PO4 A 610 " ideal model delta sigma weight residual 1.569 1.466 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O1 PO4 A 610 " pdb=" P PO4 A 610 " ideal model delta sigma weight residual 1.565 1.464 0.101 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O3 PO4 A 609 " pdb=" P PO4 A 609 " ideal model delta sigma weight residual 1.569 1.468 0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 6581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 8813 3.24 - 6.49: 238 6.49 - 9.73: 18 9.73 - 12.98: 2 12.98 - 16.22: 3 Bond angle restraints: 9074 Sorted by residual: angle pdb=" N GLN B 309 " pdb=" CA GLN B 309 " pdb=" C GLN B 309 " ideal model delta sigma weight residual 113.88 106.52 7.36 1.23e+00 6.61e-01 3.58e+01 angle pdb=" C6 PA1 C 2 " pdb=" C5 PA1 C 2 " pdb=" O5 PA1 C 2 " ideal model delta sigma weight residual 107.26 91.04 16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" CA SER A 300 " pdb=" C SER A 300 " pdb=" N LEU A 301 " ideal model delta sigma weight residual 118.17 125.27 -7.10 1.33e+00 5.65e-01 2.85e+01 angle pdb=" N GLY B 311 " pdb=" CA GLY B 311 " pdb=" C GLY B 311 " ideal model delta sigma weight residual 113.24 106.46 6.78 1.31e+00 5.83e-01 2.68e+01 angle pdb=" C ARG A 333 " pdb=" N VAL A 334 " pdb=" CA VAL A 334 " ideal model delta sigma weight residual 121.70 131.00 -9.30 1.80e+00 3.09e-01 2.67e+01 ... (remaining 9069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3593 17.53 - 35.07: 139 35.07 - 52.60: 30 52.60 - 70.14: 6 70.14 - 87.67: 6 Dihedral angle restraints: 3774 sinusoidal: 500 harmonic: 3274 Sorted by residual: dihedral pdb=" CA TYR B 351 " pdb=" C TYR B 351 " pdb=" N PRO B 352 " pdb=" CA PRO B 352 " ideal model delta harmonic sigma weight residual 180.00 139.03 40.97 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA ASP B 498 " pdb=" C ASP B 498 " pdb=" N SER B 499 " pdb=" CA SER B 499 " ideal model delta harmonic sigma weight residual -180.00 -141.68 -38.32 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" CA SER B 278 " pdb=" C SER B 278 " pdb=" N LEU B 279 " pdb=" CA LEU B 279 " ideal model delta harmonic sigma weight residual -180.00 -142.85 -37.15 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 3771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 1164 0.141 - 0.283: 38 0.283 - 0.424: 0 0.424 - 0.566: 0 0.566 - 0.707: 1 Chirality restraints: 1203 Sorted by residual: chirality pdb=" C1 GMH C 6 " pdb=" O7 GMH C 5 " pdb=" C2 GMH C 6 " pdb=" O5 GMH C 6 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.64e+01 chirality pdb=" C1 GMH C 5 " pdb=" O3 GMH C 4 " pdb=" C2 GMH C 5 " pdb=" O5 GMH C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.48 -0.08 2.00e-02 2.50e+03 1.55e+01 chirality pdb=" C5 PA1 C 2 " pdb=" C4 PA1 C 2 " pdb=" C6 PA1 C 2 " pdb=" O5 PA1 C 2 " both_signs ideal model delta sigma weight residual False -2.49 -3.20 0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 1200 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 414 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C SER B 414 " -0.063 2.00e-02 2.50e+03 pdb=" O SER B 414 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 415 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 97 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C VAL A 97 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL A 97 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 98 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 519 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ILE A 519 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 519 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 520 " 0.013 2.00e-02 2.50e+03 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 31 2.19 - 2.87: 3065 2.87 - 3.54: 10210 3.54 - 4.22: 13785 4.22 - 4.90: 21636 Nonbonded interactions: 48727 Sorted by model distance: nonbonded pdb=" O LEU A 77 " pdb=" CG2 THR A 81 " model vdw 1.511 3.460 nonbonded pdb=" O4 PA1 C 2 " pdb=" P PO4 B 601 " model vdw 1.577 3.400 nonbonded pdb=" O4 GMH C 5 " pdb=" P PO4 A 610 " model vdw 1.580 3.400 nonbonded pdb=" O1 PA1 C 1 " pdb=" P PO4 A 608 " model vdw 1.591 3.400 nonbonded pdb=" O4 GMH C 4 " pdb=" P PO4 A 609 " model vdw 1.600 3.400 ... (remaining 48722 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 31 or (resid 32 through 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 through 40 or (res \ id 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or (r \ esid 43 through 44 and (name N or name CA or name C or name O or name CB )) or r \ esid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or na \ me CB )) or resid 50 or (resid 51 through 54 and (name N or name CA or name C or \ name O or name CB )) or (resid 55 through 65 and (name N or name CA or name C o \ r name O or name CB )) or resid 66 through 79 or (resid 80 and (name N or name C \ A or name C or name O or name CB )) or resid 81 through 83 or (resid 84 through \ 86 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resi \ d 88 through 90 and (name N or name CA or name C or name O or name CB )) or resi \ d 91 through 94 or (resid 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 100 or (resid 101 and (name N or name CA or name C or \ name O or name CB )) or resid 102 through 103 or (resid 104 and (name N or name \ CA or name C or name O or name CB )) or resid 105 through 112 or (resid 113 thro \ ugh 121 and (name N or name CA or name C or name O or name CB )) or resid 122 or \ (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 4 through 144 or (resid 145 through 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 through 152 or (resid 153 through 154 and (name N \ or name CA or name C or name O or name CB )) or resid 155 or (resid 156 through \ 160 and (name N or name CA or name C or name O or name CB )) or resid 161 throug \ h 171 or (resid 172 through 175 and (name N or name CA or name C or name O or na \ me CB )) or resid 176 through 179 or (resid 180 through 187 and (name N or name \ CA or name C or name O or name CB )) or resid 188 through 191 or (resid 192 thro \ ugh 200 and (name N or name CA or name C or name O or name CB )) or resid 201 th \ rough 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) \ or resid 221 through 232 or (resid 233 through 236 and (name N or name CA or na \ me C or name O or name CB )) or resid 237 through 239 or (resid 240 and (name N \ or name CA or name C or name O or name CB )) or resid 241 or (resid 242 through \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 throug \ h 252 or (resid 253 and (name N or name CA or name C or name O or name CB )) or \ resid 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) \ or resid 256 or (resid 257 through 262 and (name N or name CA or name C or name \ O or name CB )) or resid 263 through 264 or (resid 265 through 271 and (name N \ or name CA or name C or name O or name CB )) or resid 272 through 274 or (resid \ 275 through 281 and (name N or name CA or name C or name O or name CB )) or resi \ d 282 through 302 or (resid 303 through 306 and (name N or name CA or name C or \ name O or name CB )) or resid 307 through 311 or (resid 312 through 318 and (nam \ e N or name CA or name C or name O or name CB )) or resid 319 through 321 or (re \ sid 322 through 330 and (name N or name CA or name C or name O or name CB )) or \ resid 331 through 608)) selection = (chain 'B' and (resid 11 through 17 or (resid 18 through 19 and (name N or name \ CA or name C or name O or name CB )) or resid 20 through 21 or (resid 22 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 36 or (resid 37 through 41 and (name N or name CA or name C or name O or name C \ B )) or resid 42 through 81 or (resid 82 and (name N or name CA or name C or nam \ e O or name CB )) or resid 83 through 84 or (resid 85 through 86 and (name N or \ name CA or name C or name O or name CB )) or resid 87 through 96 or (resid 97 th \ rough 99 and (name N or name CA or name C or name O or name CB )) or resid 100 t \ hrough 102 or (resid 103 through 104 and (name N or name CA or name C or name O \ or name CB )) or resid 105 through 108 or (resid 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 129 or (resid 130 through 133 \ and (name N or name CA or name C or name O or name CB )) or resid 134 or (resid \ 135 through 140 and (name N or name CA or name C or name O or name CB )) or res \ id 141 through 143 or (resid 144 through 147 and (name N or name CA or name C or \ name O or name CB )) or resid 148 or (resid 149 and (name CA or name C or name \ O or name CB )) or (resid 150 through 154 and (name N or name CA or name C or na \ me O or name CB )) or resid 155 through 161 or (resid 162 through 165 and (name \ N or name CA or name C or name O or name CB )) or resid 166 through 181 or (resi \ d 182 through 187 and (name N or name CA or name C or name O or name CB )) or re \ sid 188 through 196 or (resid 197 through 200 and (name N or name CA or name C o \ r name O or name CB )) or resid 201 through 208 or (resid 209 through 212 and (n \ ame N or name CA or name C or name O or name CB )) or resid 213 through 216 or ( \ resid 217 through 220 and (name N or name CA or name C or name O or name CB )) o \ r resid 221 through 224 or (resid 225 through 236 and (name N or name CA or name \ C or name O or name CB )) or resid 237 through 238 or (resid 239 through 240 an \ d (name N or name CA or name C or name O or name CB )) or resid 241 through 251 \ or (resid 252 through 253 and (name N or name CA or name C or name O or name CB \ )) or resid 254 through 266 or (resid 267 through 271 and (name N or name CA or \ name C or name O or name CB )) or resid 272 through 282 or (resid 283 and (name \ N or name CA or name C or name O or name CB )) or resid 284 through 287 or (resi \ d 288 through 291 and (name N or name CA or name C or name O or name CB )) or re \ sid 292 through 294 or (resid 295 and (name N or name CA or name C or name O or \ name CB )) or resid 296 through 304 or (resid 305 through 306 and (name N or nam \ e CA or name C or name O or name CB )) or resid 307 through 309 or (resid 310 an \ d (name N or name CA or name C or name O or name CB )) or (resid 311 through 318 \ and (name N or name CA or name C or name O or name CB )) or resid 319 through 3 \ 20 or (resid 321 through 330 and (name N or name CA or name C or name O or name \ CB )) or resid 331 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.710 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 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 : 0.010 0.474 6599 Z= 0.747 Angle : 1.294 16.223 9092 Z= 0.753 Chirality : 0.064 0.707 1203 Planarity : 0.005 0.045 1225 Dihedral : 12.843 87.669 1644 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 46.64 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.14 % Favored : 86.16 % Rotamer: Outliers : 0.48 % Allowed : 11.06 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 7.69 % Twisted General : 0.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.82 (0.16), residues: 1134 helix: -3.92 (0.11), residues: 718 sheet: -3.39 (0.83), residues: 23 loop : -3.35 (0.23), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 238 TYR 0.028 0.002 TYR B 268 PHE 0.036 0.003 PHE A 220 TRP 0.017 0.003 TRP B 17 HIS 0.021 0.006 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.44 ( 6586) covalent geometry : angle 1.26350 / 0.75 ( 9074) hydrogen bonds : bond 0.19166 / 13.80 ( 536) hydrogen bonds : angle 12.63068 / 9.33 ( 1572) glycosidic custom : bond 0.02010 / 1.05 ( 5) glycosidic custom : angle 6.50724 / 4.13 ( 15) Misc. bond : bond 0.18511 / 9.71 ( 7) link_ALPHA1-3 : bond 0.00816 / 0.43 ( 1) link_ALPHA1-3 : angle 6.10918 / 3.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LEU cc_start: 0.7111 (tt) cc_final: 0.6893 (tt) REVERT: A 302 THR cc_start: 0.7128 (p) cc_final: 0.6889 (p) REVERT: B 75 MET cc_start: 0.5169 (mmp) cc_final: 0.4867 (mmp) REVERT: B 98 MET cc_start: 0.7031 (mmt) cc_final: 0.6769 (mmm) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.0754 time to fit residues: 13.6976 Evaluate side-chains 91 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.0870 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.109657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.094050 restraints weight = 31557.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.094334 restraints weight = 24088.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.094788 restraints weight = 22056.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.096284 restraints weight = 17142.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.096250 restraints weight = 14159.477| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6599 Z= 0.195 Angle : 0.835 10.948 9092 Z= 0.436 Chirality : 0.049 0.293 1203 Planarity : 0.005 0.044 1225 Dihedral : 8.455 70.244 1189 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 0.48 % Allowed : 3.85 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.22), residues: 1134 helix: -1.35 (0.17), residues: 726 sheet: -3.51 (0.68), residues: 32 loop : -2.50 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 310 TYR 0.009 0.001 TYR B 130 PHE 0.038 0.003 PHE A 161 TRP 0.014 0.002 TRP B 17 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.19 ( 6586) covalent geometry : angle 0.80748 / 0.43 ( 9074) hydrogen bonds : bond 0.06296 / 4.46 ( 536) hydrogen bonds : angle 6.89642 / 5.14 ( 1572) glycosidic custom : bond 0.01185 / 0.63 ( 5) glycosidic custom : angle 5.13037 / 2.70 ( 15) Misc. bond : bond 0.00478 / 0.25 ( 7) link_ALPHA1-3 : bond 0.00869 / 0.46 ( 1) link_ALPHA1-3 : angle 3.12290 / 1.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 302 THR cc_start: 0.7213 (p) cc_final: 0.6919 (p) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.0554 time to fit residues: 9.2725 Evaluate side-chains 89 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 93 optimal weight: 50.0000 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 40.0000 chunk 77 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 6 optimal weight: 0.2980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN B 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.107524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.092559 restraints weight = 31926.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.092688 restraints weight = 26834.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.093077 restraints weight = 23685.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.093567 restraints weight = 19615.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.093601 restraints weight = 18554.829| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6599 Z= 0.166 Angle : 0.691 9.629 9092 Z= 0.359 Chirality : 0.045 0.225 1203 Planarity : 0.004 0.055 1225 Dihedral : 7.181 78.566 1189 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.24), residues: 1134 helix: 0.07 (0.18), residues: 744 sheet: -3.67 (0.50), residues: 49 loop : -2.27 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 148 TYR 0.012 0.001 TYR B 268 PHE 0.034 0.002 PHE A 161 TRP 0.017 0.002 TRP A 66 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 ( 6586) covalent geometry : angle 0.67400 / 0.36 ( 9074) hydrogen bonds : bond 0.05248 / 3.71 ( 536) hydrogen bonds : angle 5.80505 / 4.31 ( 1572) glycosidic custom : bond 0.00852 / 0.53 ( 5) glycosidic custom : angle 3.49879 / 1.92 ( 15) Misc. bond : bond 0.00072 / 0.04 ( 7) link_ALPHA1-3 : bond 0.00451 / 0.24 ( 1) link_ALPHA1-3 : angle 3.57070 / 1.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.177 Fit side-chains REVERT: A 35 ILE cc_start: 0.9074 (mt) cc_final: 0.8802 (mt) REVERT: A 302 THR cc_start: 0.7506 (p) cc_final: 0.7245 (p) REVERT: B 295 MET cc_start: 0.8545 (tmm) cc_final: 0.7934 (tmm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0504 time to fit residues: 7.6323 Evaluate side-chains 87 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 103 optimal weight: 50.0000 chunk 31 optimal weight: 0.3980 chunk 52 optimal weight: 50.0000 chunk 4 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 overall best weight: 3.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.106521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.090522 restraints weight = 32264.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.091345 restraints weight = 24674.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.091968 restraints weight = 19958.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.092266 restraints weight = 16874.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.092773 restraints weight = 15112.643| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6599 Z= 0.160 Angle : 0.659 8.328 9092 Z= 0.342 Chirality : 0.044 0.160 1203 Planarity : 0.004 0.039 1225 Dihedral : 6.599 69.058 1189 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.25), residues: 1134 helix: 0.72 (0.19), residues: 743 sheet: -3.31 (0.57), residues: 55 loop : -1.97 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 238 TYR 0.011 0.001 TYR B 83 PHE 0.035 0.002 PHE A 157 TRP 0.049 0.003 TRP A 66 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 ( 6586) covalent geometry : angle 0.64371 / 0.34 ( 9074) hydrogen bonds : bond 0.04958 / 3.52 ( 536) hydrogen bonds : angle 5.32734 / 3.98 ( 1572) glycosidic custom : bond 0.00924 / 0.54 ( 5) glycosidic custom : angle 3.25039 / 1.75 ( 15) Misc. bond : bond 0.00081 / 0.05 ( 7) link_ALPHA1-3 : bond 0.00519 / 0.27 ( 1) link_ALPHA1-3 : angle 3.43108 / 1.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.246 Fit side-chains REVERT: A 157 PHE cc_start: 0.7784 (m-80) cc_final: 0.7472 (m-80) REVERT: B 134 GLN cc_start: 0.7998 (tp40) cc_final: 0.7579 (tp40) REVERT: B 256 GLN cc_start: 0.7177 (mm110) cc_final: 0.6922 (mm110) REVERT: B 295 MET cc_start: 0.8484 (tmm) cc_final: 0.8219 (tmm) REVERT: B 296 ARG cc_start: 0.7148 (tmt170) cc_final: 0.6774 (tmt170) REVERT: B 302 THR cc_start: 0.7201 (m) cc_final: 0.6885 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0564 time to fit residues: 8.3499 Evaluate side-chains 86 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 67 optimal weight: 30.0000 chunk 86 optimal weight: 0.9980 chunk 39 optimal weight: 50.0000 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.107283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.092343 restraints weight = 32412.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.092660 restraints weight = 25333.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.093087 restraints weight = 22169.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.094383 restraints weight = 18229.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.094212 restraints weight = 14903.710| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6599 Z= 0.126 Angle : 0.601 7.180 9092 Z= 0.305 Chirality : 0.043 0.170 1203 Planarity : 0.003 0.037 1225 Dihedral : 6.321 69.293 1189 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1134 helix: 1.17 (0.19), residues: 743 sheet: -2.70 (0.61), residues: 58 loop : -1.83 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.006 0.001 TYR B 162 PHE 0.024 0.001 PHE B 288 TRP 0.021 0.002 TRP A 66 HIS 0.001 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 ( 6586) covalent geometry : angle 0.58582 / 0.30 ( 9074) hydrogen bonds : bond 0.04424 / 3.13 ( 536) hydrogen bonds : angle 4.91101 / 3.67 ( 1572) glycosidic custom : bond 0.00911 / 0.54 ( 5) glycosidic custom : angle 3.02548 / 1.67 ( 15) Misc. bond : bond 0.00057 / 0.03 ( 7) link_ALPHA1-3 : bond 0.00194 / 0.10 ( 1) link_ALPHA1-3 : angle 3.41819 / 1.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.179 Fit side-chains REVERT: A 157 PHE cc_start: 0.7728 (m-80) cc_final: 0.7346 (m-80) REVERT: B 302 THR cc_start: 0.7279 (m) cc_final: 0.6986 (p) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0630 time to fit residues: 9.5792 Evaluate side-chains 86 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 26 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 106 optimal weight: 8.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.107668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.091915 restraints weight = 32487.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092624 restraints weight = 24481.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.093304 restraints weight = 19689.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.093683 restraints weight = 16451.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.094178 restraints weight = 14420.901| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6599 Z= 0.136 Angle : 0.620 8.609 9092 Z= 0.316 Chirality : 0.043 0.158 1203 Planarity : 0.003 0.037 1225 Dihedral : 6.176 74.133 1189 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1134 helix: 1.40 (0.19), residues: 745 sheet: -2.82 (0.64), residues: 58 loop : -1.70 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 238 TYR 0.015 0.001 TYR B 83 PHE 0.019 0.001 PHE A 272 TRP 0.031 0.002 TRP A 66 HIS 0.002 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 6586) covalent geometry : angle 0.60541 / 0.31 ( 9074) hydrogen bonds : bond 0.04402 / 3.11 ( 536) hydrogen bonds : angle 4.75288 / 3.56 ( 1572) glycosidic custom : bond 0.00700 / 0.37 ( 5) glycosidic custom : angle 2.94250 / 1.62 ( 15) Misc. bond : bond 0.00051 / 0.03 ( 7) link_ALPHA1-3 : bond 0.00380 / 0.20 ( 1) link_ALPHA1-3 : angle 3.37194 / 1.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7488 (tmm) cc_final: 0.7239 (tmm) REVERT: B 295 MET cc_start: 0.8494 (tmm) cc_final: 0.7800 (tmm) REVERT: B 296 ARG cc_start: 0.7442 (tmt170) cc_final: 0.6866 (tmt170) REVERT: B 302 THR cc_start: 0.7190 (m) cc_final: 0.6895 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0608 time to fit residues: 8.9347 Evaluate side-chains 89 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 0.0010 chunk 29 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.105610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.093460 restraints weight = 32313.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.092465 restraints weight = 53025.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.092799 restraints weight = 45066.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.092620 restraints weight = 38485.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.092651 restraints weight = 36946.982| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6599 Z= 0.157 Angle : 0.624 6.898 9092 Z= 0.322 Chirality : 0.043 0.156 1203 Planarity : 0.004 0.037 1225 Dihedral : 6.026 72.006 1189 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1134 helix: 1.34 (0.19), residues: 759 sheet: -2.16 (0.83), residues: 42 loop : -2.00 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 238 TYR 0.009 0.001 TYR A 83 PHE 0.025 0.002 PHE B 288 TRP 0.021 0.003 TRP A 66 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 ( 6586) covalent geometry : angle 0.60851 / 0.32 ( 9074) hydrogen bonds : bond 0.04631 / 3.27 ( 536) hydrogen bonds : angle 4.81566 / 3.59 ( 1572) glycosidic custom : bond 0.00707 / 0.47 ( 5) glycosidic custom : angle 3.10497 / 1.71 ( 15) Misc. bond : bond 0.00065 / 0.04 ( 7) link_ALPHA1-3 : bond 0.00295 / 0.16 ( 1) link_ALPHA1-3 : angle 3.33093 / 1.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.7112 (m-80) cc_final: 0.6696 (m-80) REVERT: A 196 MET cc_start: 0.7277 (tpp) cc_final: 0.6995 (tpt) REVERT: B 295 MET cc_start: 0.8259 (tmm) cc_final: 0.7691 (tmm) REVERT: B 296 ARG cc_start: 0.7418 (tmt170) cc_final: 0.6526 (tmt170) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0615 time to fit residues: 8.8275 Evaluate side-chains 84 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 0.0050 chunk 67 optimal weight: 30.0000 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 0.1980 chunk 54 optimal weight: 50.0000 chunk 96 optimal weight: 8.9990 chunk 4 optimal weight: 0.0370 chunk 112 optimal weight: 0.8980 chunk 98 optimal weight: 50.0000 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.107112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.091875 restraints weight = 32329.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.092491 restraints weight = 25090.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.093175 restraints weight = 20861.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.093464 restraints weight = 17810.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.093805 restraints weight = 15902.806| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6599 Z= 0.121 Angle : 0.577 6.591 9092 Z= 0.291 Chirality : 0.042 0.174 1203 Planarity : 0.003 0.034 1225 Dihedral : 5.584 78.483 1189 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1134 helix: 1.71 (0.19), residues: 750 sheet: -2.29 (0.81), residues: 39 loop : -2.10 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.006 0.001 TYR B 162 PHE 0.020 0.001 PHE A 272 TRP 0.015 0.001 TRP B 17 HIS 0.001 0.000 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 ( 6586) covalent geometry : angle 0.56297 / 0.29 ( 9074) hydrogen bonds : bond 0.03989 / 2.82 ( 536) hydrogen bonds : angle 4.42669 / 3.31 ( 1572) glycosidic custom : bond 0.00845 / 0.49 ( 5) glycosidic custom : angle 2.83779 / 1.56 ( 15) Misc. bond : bond 0.00033 / 0.02 ( 7) link_ALPHA1-3 : bond 0.00085 / 0.04 ( 1) link_ALPHA1-3 : angle 3.01786 / 1.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.5819 (m-30) cc_final: 0.4917 (p0) REVERT: A 74 LEU cc_start: 0.7063 (tt) cc_final: 0.6771 (tt) REVERT: A 78 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7432 (tpp80) REVERT: A 196 MET cc_start: 0.7130 (tpp) cc_final: 0.6928 (tpt) REVERT: B 98 MET cc_start: 0.7756 (mtp) cc_final: 0.7524 (tpp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0683 time to fit residues: 10.1228 Evaluate side-chains 88 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 0.0270 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 40.0000 chunk 73 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 chunk 32 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.104847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.088393 restraints weight = 32303.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.089398 restraints weight = 24080.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.090137 restraints weight = 18976.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.090514 restraints weight = 15728.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.090619 restraints weight = 13863.514| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6599 Z= 0.162 Angle : 0.620 7.242 9092 Z= 0.320 Chirality : 0.043 0.141 1203 Planarity : 0.004 0.036 1225 Dihedral : 5.892 82.820 1189 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1134 helix: 1.57 (0.19), residues: 764 sheet: -2.19 (0.74), residues: 48 loop : -2.06 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 236 TYR 0.007 0.001 TYR B 83 PHE 0.009 0.001 PHE B 308 TRP 0.022 0.002 TRP B 17 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 ( 6586) covalent geometry : angle 0.60545 / 0.32 ( 9074) hydrogen bonds : bond 0.04453 / 3.14 ( 536) hydrogen bonds : angle 4.63018 / 3.46 ( 1572) glycosidic custom : bond 0.00702 / 0.45 ( 5) glycosidic custom : angle 3.03902 / 1.66 ( 15) Misc. bond : bond 0.00064 / 0.04 ( 7) link_ALPHA1-3 : bond 0.00329 / 0.17 ( 1) link_ALPHA1-3 : angle 3.27737 / 1.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7534 (tmm) cc_final: 0.7323 (tmm) REVERT: A 196 MET cc_start: 0.7671 (tpp) cc_final: 0.7360 (tpt) REVERT: A 242 MET cc_start: 0.7426 (mmm) cc_final: 0.7161 (mtt) REVERT: B 295 MET cc_start: 0.8654 (tmm) cc_final: 0.8129 (tmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0507 time to fit residues: 7.6615 Evaluate side-chains 81 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 50.0000 chunk 108 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.106753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.090639 restraints weight = 31390.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.091493 restraints weight = 24124.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.091938 restraints weight = 19439.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.092570 restraints weight = 16734.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.092985 restraints weight = 14584.014| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6599 Z= 0.123 Angle : 0.599 8.988 9092 Z= 0.300 Chirality : 0.042 0.155 1203 Planarity : 0.003 0.036 1225 Dihedral : 5.636 87.044 1189 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1134 helix: 1.78 (0.19), residues: 764 sheet: -2.23 (0.83), residues: 38 loop : -2.07 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 236 TYR 0.007 0.001 TYR B 162 PHE 0.012 0.001 PHE B 23 TRP 0.013 0.001 TRP B 17 HIS 0.002 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 ( 6586) covalent geometry : angle 0.58554 / 0.30 ( 9074) hydrogen bonds : bond 0.04054 / 2.86 ( 536) hydrogen bonds : angle 4.39843 / 3.28 ( 1572) glycosidic custom : bond 0.00713 / 0.42 ( 5) glycosidic custom : angle 2.88552 / 1.57 ( 15) Misc. bond : bond 0.00041 / 0.02 ( 7) link_ALPHA1-3 : bond 0.00140 / 0.07 ( 1) link_ALPHA1-3 : angle 2.91478 / 1.57 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.5818 (m-30) cc_final: 0.4815 (p0) REVERT: A 75 MET cc_start: 0.7406 (tmm) cc_final: 0.7161 (tmm) REVERT: A 196 MET cc_start: 0.7310 (tpp) cc_final: 0.7037 (tpt) REVERT: B 295 MET cc_start: 0.8424 (tmm) cc_final: 0.8207 (tmm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0528 time to fit residues: 8.1745 Evaluate side-chains 84 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 38 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 40.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.103730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.088596 restraints weight = 32249.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.089392 restraints weight = 24816.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.089948 restraints weight = 20151.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.090406 restraints weight = 17218.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.090505 restraints weight = 15229.943| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6599 Z= 0.176 Angle : 0.653 9.018 9092 Z= 0.336 Chirality : 0.044 0.129 1203 Planarity : 0.004 0.053 1225 Dihedral : 5.979 83.866 1189 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1134 helix: 1.51 (0.19), residues: 772 sheet: -2.39 (0.70), residues: 49 loop : -1.96 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 78 TYR 0.007 0.001 TYR B 83 PHE 0.010 0.001 PHE B 308 TRP 0.020 0.002 TRP B 17 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 ( 6586) covalent geometry : angle 0.63890 / 0.33 ( 9074) hydrogen bonds : bond 0.04633 / 3.27 ( 536) hydrogen bonds : angle 4.64095 / 3.46 ( 1572) glycosidic custom : bond 0.00611 / 0.37 ( 5) glycosidic custom : angle 3.01556 / 1.65 ( 15) Misc. bond : bond 0.00140 / 0.07 ( 7) link_ALPHA1-3 : bond 0.00186 / 0.10 ( 1) link_ALPHA1-3 : angle 3.27545 / 1.76 ( 3) =============================================================================== Job complete usr+sys time: 968.05 seconds wall clock time: 17 minutes 14.07 seconds (1034.07 seconds total)