Starting phenix.real_space_refine on Thu Jul 2 10:29:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2u_27150/07_2026/8d2u_27150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2u_27150/07_2026/8d2u_27150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2026/8d2u_27150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2026/8d2u_27150.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2026/8d2u_27150.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2026/8d2u_27150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2026/8d2u_27150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2u_27150/07_2026/8d2u_27150.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1613 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 38 5.16 5 Na 1 4.78 5 C 4504 2.51 5 N 1023 2.21 5 O 1295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6862 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3431 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 7, 'GLN:plan1': 5, 'HIS:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 460, 3431 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 7, 'GLN:plan1': 5, 'HIS:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 112 bond proxies already assigned to first conformer: 3483 Chain: "B" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1411 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1415 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 531 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 472 Unusual residues: {' NA': 1, 'LMT': 15, 'ZGS': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 41 Conformer: "B" Number of residues, atoms: 17, 472 Unusual residues: {' NA': 1, 'LMT': 15, 'ZGS': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 41 bond proxies already assigned to first conformer: 417 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AGLN A 345 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 345 " occ=0.50 residue: pdb=" N ATRP A 400 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 400 " occ=0.50 residue: pdb=" N APHE A 449 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 449 " occ=0.50 residue: pdb=" C1 ALMT A 602 " occ=0.50 ... (46 atoms not shown) pdb=" O6'BLMT A 602 " occ=0.50 residue: pdb=" C1 ALMT A 608 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 608 " occ=0.50 Time building chain proxies: 2.00, per 1000 atoms: 0.29 Number of scatterers: 6862 At special positions: 0 Unit cell: (69.208, 74.272, 142.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 1 15.00 Na 1 11.00 O 1295 8.00 N 1023 7.00 C 4504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 388.8 milliseconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 10 sheets defined 45.3% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 47 through 68 removed outlier: 3.835A pdb=" N GLN A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 100 removed outlier: 3.958A pdb=" N ARG A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 109 through 128 Proline residue: A 118 - end of helix removed outlier: 3.630A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.645A pdb=" N TRP A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.511A pdb=" N SER A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 200 removed outlier: 3.810A pdb=" N THR A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 196 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 262 removed outlier: 3.502A pdb=" N VAL A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 removed outlier: 3.510A pdb=" N HIS A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 319 removed outlier: 4.862A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.657A pdb=" N VAL A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.862A pdb=" N THR A 349 " --> pdb=" O AGLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.974A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 removed outlier: 4.520A pdb=" N PHE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 414 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 419 through 451 removed outlier: 3.851A pdb=" N SER A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.503A pdb=" N SER A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.636A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.023A pdb=" N LYS B 11 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 32 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR B 48 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.889A pdb=" N ASN B 134 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR B 166 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.861A pdb=" N TRP B 143 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 33 through 39 removed outlier: 6.644A pdb=" N VAL C 34 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA C 49 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TRP C 36 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.997A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.997A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 149 through 151 removed outlier: 4.779A pdb=" N ALA C 184 " --> pdb=" O VAL C 200 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1100 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: 0.70 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 996 1.30 - 1.43: 1851 1.43 - 1.56: 4027 1.56 - 1.68: 111 1.68 - 1.81: 55 Bond restraints: 7040 Sorted by residual: bond pdb=" C1B LMT A 612 " pdb=" O5B LMT A 612 " ideal model delta sigma weight residual 1.393 1.521 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C1BALMT A 608 " pdb=" O5BALMT A 608 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C1BBLMT A 608 " pdb=" O5BBLMT A 608 " ideal model delta sigma weight residual 1.393 1.515 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1B LMT A 611 " pdb=" O5B LMT A 611 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1B LMT A 616 " pdb=" O5B LMT A 616 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 7035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.86: 9423 5.86 - 11.72: 140 11.72 - 17.58: 5 17.58 - 23.44: 1 23.44 - 29.30: 2 Bond angle restraints: 9571 Sorted by residual: angle pdb=" C09 ZGS A 601 " pdb=" C10 ZGS A 601 " pdb=" C11 ZGS A 601 " ideal model delta sigma weight residual 127.16 156.46 -29.30 3.00e+00 1.11e-01 9.54e+01 angle pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " ideal model delta sigma weight residual 127.52 151.01 -23.49 3.00e+00 1.11e-01 6.13e+01 angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 110.70 132.09 -21.39 3.00e+00 1.11e-01 5.08e+01 angle pdb=" C03 ZGS A 601 " pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " ideal model delta sigma weight residual 127.34 142.92 -15.58 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C02 ZGS A 601 " pdb=" C03 ZGS A 601 " pdb=" C04 ZGS A 601 " ideal model delta sigma weight residual 127.67 112.16 15.51 3.00e+00 1.11e-01 2.67e+01 ... (remaining 9566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3559 17.27 - 34.55: 269 34.55 - 51.82: 75 51.82 - 69.09: 27 69.09 - 86.37: 4 Dihedral angle restraints: 3934 sinusoidal: 1470 harmonic: 2464 Sorted by residual: dihedral pdb=" CA LEU B 132 " pdb=" C LEU B 132 " pdb=" N PRO B 133 " pdb=" CA PRO B 133 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE C 58 " pdb=" C PHE C 58 " pdb=" N GLU C 59 " pdb=" CA GLU C 59 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLY C 54 " pdb=" C GLY C 54 " pdb=" N PRO C 55 " pdb=" CA PRO C 55 " ideal model delta harmonic sigma weight residual 180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 3931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 898 0.060 - 0.120: 195 0.120 - 0.180: 42 0.180 - 0.240: 3 0.240 - 0.300: 2 Chirality restraints: 1140 Sorted by residual: chirality pdb=" C1B LMT B 301 " pdb=" C2B LMT B 301 " pdb=" O1B LMT B 301 " pdb=" O5B LMT B 301 " both_signs ideal model delta sigma weight residual False -2.20 -2.50 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C4' LMT B 301 " pdb=" C3' LMT B 301 " pdb=" C5' LMT B 301 " pdb=" O1B LMT B 301 " both_signs ideal model delta sigma weight residual False -2.55 -2.26 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C1B LMT A 605 " pdb=" C2B LMT A 605 " pdb=" O1B LMT A 605 " pdb=" O5B LMT A 605 " both_signs ideal model delta sigma weight residual False -2.20 -2.42 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1137 not shown) Planarity restraints: 1132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 398 " -0.045 5.00e-02 4.00e+02 6.65e-02 7.09e+00 pdb=" N PRO A 399 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO C 47 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 374 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 375 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.032 5.00e-02 4.00e+02 ... (remaining 1129 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2310 2.85 - 3.37: 6004 3.37 - 3.88: 11522 3.88 - 4.39: 12717 4.39 - 4.90: 22541 Nonbonded interactions: 55094 Sorted by model distance: nonbonded pdb=" O TYR A 43 " pdb=" OH TYR A 159 " model vdw 2.344 3.040 nonbonded pdb=" O THR A 381 " pdb=" OG SER A 385 " model vdw 2.347 3.040 nonbonded pdb=" O SER A 439 " pdb=" OG SER A 443 " model vdw 2.354 3.040 nonbonded pdb=" O SER A 132 " pdb=" O2B LMT A 607 " model vdw 2.362 3.040 nonbonded pdb=" OH TYR A 43 " pdb=" OG1 THR A 163 " model vdw 2.372 3.040 ... (remaining 55089 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.790 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.012 0.128 7044 Z= 0.615 Angle : 1.445 29.303 9579 Z= 0.602 Chirality : 0.054 0.300 1140 Planarity : 0.007 0.067 1132 Dihedral : 14.511 86.367 2352 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.99 % Allowed : 7.06 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.64 (0.24), residues: 865 helix: -1.03 (0.22), residues: 367 sheet: -1.07 (0.38), residues: 170 loop : -2.88 (0.28), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 92 TYR 0.017 0.002 TYR A 50 PHE 0.031 0.002 PHE C 38 TRP 0.015 0.002 TRP A 140 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.01227 / 0.61 ( 7040) covalent geometry : angle 1.44504 / 0.60 ( 9571) SS BOND : bond 0.00322 / 0.16 ( 4) SS BOND : angle 0.94582 / 0.49 ( 8) hydrogen bonds : bond 0.12769 / 8.35 ( 375) hydrogen bonds : angle 7.06443 / 5.20 ( 1100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.152 Fit side-chains REVERT: A 276 MET cc_start: 0.6336 (mmm) cc_final: 0.5739 (mmm) REVERT: A 339 LEU cc_start: 0.7642 (mt) cc_final: 0.7297 (mt) REVERT: B 61 SER cc_start: 0.8006 (m) cc_final: 0.7796 (p) REVERT: B 91 LYS cc_start: 0.8375 (mttt) cc_final: 0.8109 (mtpt) REVERT: C 13 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7594 (mmt-90) REVERT: C 23 LYS cc_start: 0.7936 (tttm) cc_final: 0.7612 (mtpt) outliers start: 6 outliers final: 1 residues processed: 147 average time/residue: 0.0622 time to fit residues: 12.3294 Evaluate side-chains 104 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.0060 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 102 ASN B 110 GLN C 50 ASN C 57 GLN C 74 GLN C 99 ASN C 166 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.180132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144822 restraints weight = 22698.175| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 4.82 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (13 function evaluations) r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7044 Z= 0.154 Angle : 0.633 7.046 9579 Z= 0.310 Chirality : 0.042 0.249 1140 Planarity : 0.006 0.060 1132 Dihedral : 12.783 59.637 1140 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.64 % Allowed : 13.79 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.27), residues: 865 helix: 0.60 (0.25), residues: 386 sheet: -1.12 (0.35), residues: 197 loop : -2.43 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 108 TYR 0.011 0.001 TYR A 251 PHE 0.018 0.002 PHE A 144 TRP 0.021 0.002 TRP A 103 HIS 0.001 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 7040) covalent geometry : angle 0.63282 / 0.31 ( 9571) SS BOND : bond 0.00156 / 0.08 ( 4) SS BOND : angle 0.40423 / 0.24 ( 8) hydrogen bonds : bond 0.03688 / 2.39 ( 375) hydrogen bonds : angle 4.79266 / 3.54 ( 1100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.147 Fit side-chains REVERT: A 108 ARG cc_start: 0.7655 (mtp180) cc_final: 0.7403 (mtp180) REVERT: A 276 MET cc_start: 0.6498 (mmm) cc_final: 0.6129 (mmt) REVERT: A 411 LYS cc_start: 0.8125 (tmmt) cc_final: 0.7851 (tmtt) REVERT: B 105 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6402 (tm-30) REVERT: C 81 ILE cc_start: 0.8470 (mm) cc_final: 0.8144 (mm) REVERT: C 95 TRP cc_start: 0.7476 (p-90) cc_final: 0.7271 (p-90) outliers start: 10 outliers final: 3 residues processed: 114 average time/residue: 0.0756 time to fit residues: 11.4015 Evaluate side-chains 105 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140860 restraints weight = 19847.878| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.52 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7044 Z= 0.155 Angle : 0.621 7.411 9579 Z= 0.303 Chirality : 0.042 0.237 1140 Planarity : 0.005 0.062 1132 Dihedral : 11.905 59.437 1139 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.96 % Allowed : 13.46 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.28), residues: 865 helix: 1.22 (0.26), residues: 384 sheet: -1.10 (0.36), residues: 197 loop : -2.35 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 40 TYR 0.013 0.001 TYR A 251 PHE 0.018 0.002 PHE B 89 TRP 0.023 0.002 TRP A 103 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 7040) covalent geometry : angle 0.62148 / 0.30 ( 9571) SS BOND : bond 0.00217 / 0.11 ( 4) SS BOND : angle 0.31151 / 0.17 ( 8) hydrogen bonds : bond 0.03559 / 2.33 ( 375) hydrogen bonds : angle 4.51166 / 3.33 ( 1100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.207 Fit side-chains REVERT: A 276 MET cc_start: 0.6648 (mmm) cc_final: 0.6167 (mmt) REVERT: A 411 LYS cc_start: 0.8263 (tmmt) cc_final: 0.7982 (tmtt) REVERT: B 105 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6287 (tm-30) REVERT: C 81 ILE cc_start: 0.8433 (mm) cc_final: 0.8095 (mm) REVERT: C 95 TRP cc_start: 0.7720 (p-90) cc_final: 0.7344 (p-90) outliers start: 18 outliers final: 11 residues processed: 115 average time/residue: 0.0792 time to fit residues: 12.0600 Evaluate side-chains 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 84 optimal weight: 0.5980 chunk 22 optimal weight: 0.0040 chunk 21 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.176549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139134 restraints weight = 17028.764| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 4.09 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (16 function evaluations) r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7044 Z= 0.116 Angle : 0.583 6.334 9579 Z= 0.281 Chirality : 0.040 0.213 1140 Planarity : 0.005 0.061 1132 Dihedral : 11.388 59.902 1139 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.64 % Allowed : 15.11 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.29), residues: 865 helix: 1.52 (0.26), residues: 387 sheet: -1.11 (0.36), residues: 199 loop : -2.28 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 40 TYR 0.011 0.001 TYR A 251 PHE 0.015 0.001 PHE A 298 TRP 0.013 0.001 TRP A 140 HIS 0.001 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7040) covalent geometry : angle 0.58273 / 0.28 ( 9571) SS BOND : bond 0.00256 / 0.13 ( 4) SS BOND : angle 0.31779 / 0.18 ( 8) hydrogen bonds : bond 0.03217 / 2.11 ( 375) hydrogen bonds : angle 4.28277 / 3.17 ( 1100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.282 Fit side-chains REVERT: A 170 GLN cc_start: 0.8369 (tp40) cc_final: 0.7894 (tp-100) REVERT: A 276 MET cc_start: 0.6631 (mmm) cc_final: 0.6113 (mmt) REVERT: A 303 LEU cc_start: 0.8821 (mt) cc_final: 0.8555 (mp) REVERT: A 347 PHE cc_start: 0.8685 (t80) cc_final: 0.8479 (t80) REVERT: A 411 LYS cc_start: 0.8493 (tmmt) cc_final: 0.8287 (tmtt) REVERT: B 105 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6075 (tm-30) REVERT: C 81 ILE cc_start: 0.8393 (mm) cc_final: 0.8053 (mm) REVERT: C 95 TRP cc_start: 0.7703 (p-90) cc_final: 0.7350 (p-90) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.0801 time to fit residues: 11.7216 Evaluate side-chains 108 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.173777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136529 restraints weight = 18780.305| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 4.47 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7044 Z= 0.149 Angle : 0.605 6.787 9579 Z= 0.292 Chirality : 0.041 0.187 1140 Planarity : 0.005 0.063 1132 Dihedral : 11.256 59.955 1139 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.28 % Allowed : 14.78 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.29), residues: 865 helix: 1.61 (0.26), residues: 386 sheet: -1.00 (0.37), residues: 197 loop : -2.32 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.011 0.001 TYR A 251 PHE 0.019 0.001 PHE B 89 TRP 0.015 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7040) covalent geometry : angle 0.60475 / 0.29 ( 9571) SS BOND : bond 0.00211 / 0.10 ( 4) SS BOND : angle 0.35581 / 0.19 ( 8) hydrogen bonds : bond 0.03400 / 2.23 ( 375) hydrogen bonds : angle 4.32621 / 3.19 ( 1100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.157 Fit side-chains REVERT: A 170 GLN cc_start: 0.8405 (tp40) cc_final: 0.7950 (tp-100) REVERT: A 263 LYS cc_start: 0.8346 (mmpt) cc_final: 0.8084 (mmmt) REVERT: A 276 MET cc_start: 0.6576 (mmm) cc_final: 0.6042 (mmt) REVERT: A 303 LEU cc_start: 0.8894 (mt) cc_final: 0.8642 (mp) REVERT: B 105 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6184 (tm-30) REVERT: C 81 ILE cc_start: 0.8404 (mm) cc_final: 0.8082 (mm) REVERT: C 95 TRP cc_start: 0.7775 (p-90) cc_final: 0.7438 (p-90) outliers start: 20 outliers final: 14 residues processed: 121 average time/residue: 0.0890 time to fit residues: 14.0048 Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137522 restraints weight = 15113.938| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.29 r_work: 0.3254 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7044 Z= 0.162 Angle : 0.617 7.454 9579 Z= 0.299 Chirality : 0.041 0.151 1140 Planarity : 0.005 0.065 1132 Dihedral : 11.034 59.554 1139 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.12 % Allowed : 15.11 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.29), residues: 865 helix: 1.68 (0.26), residues: 382 sheet: -0.96 (0.37), residues: 197 loop : -2.32 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TYR 0.012 0.001 TYR A 251 PHE 0.019 0.001 PHE B 89 TRP 0.015 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 7040) covalent geometry : angle 0.61631 / 0.30 ( 9571) SS BOND : bond 0.00347 / 0.17 ( 4) SS BOND : angle 1.08920 / 0.60 ( 8) hydrogen bonds : bond 0.03435 / 2.23 ( 375) hydrogen bonds : angle 4.36933 / 3.21 ( 1100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.232 Fit side-chains REVERT: A 263 LYS cc_start: 0.8297 (mmpt) cc_final: 0.8051 (mmmt) REVERT: A 276 MET cc_start: 0.6382 (mmm) cc_final: 0.5783 (mmt) REVERT: A 303 LEU cc_start: 0.8905 (mt) cc_final: 0.8640 (mp) REVERT: B 105 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: C 81 ILE cc_start: 0.8457 (mm) cc_final: 0.8119 (mm) REVERT: C 95 TRP cc_start: 0.8306 (p-90) cc_final: 0.7865 (p-90) outliers start: 19 outliers final: 15 residues processed: 117 average time/residue: 0.0810 time to fit residues: 12.5222 Evaluate side-chains 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 66 optimal weight: 0.0030 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 79 optimal weight: 6.9990 overall best weight: 0.1946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145338 restraints weight = 24245.238| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 4.81 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7044 Z= 0.105 Angle : 0.566 7.506 9579 Z= 0.272 Chirality : 0.039 0.132 1140 Planarity : 0.005 0.062 1132 Dihedral : 10.407 59.258 1139 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.96 % Allowed : 15.27 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.29), residues: 865 helix: 1.84 (0.26), residues: 388 sheet: -0.99 (0.37), residues: 199 loop : -2.29 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 40 TYR 0.010 0.001 TYR A 251 PHE 0.014 0.001 PHE C 38 TRP 0.014 0.001 TRP A 344 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 7040) covalent geometry : angle 0.56549 / 0.27 ( 9571) SS BOND : bond 0.00341 / 0.17 ( 4) SS BOND : angle 0.86894 / 0.48 ( 8) hydrogen bonds : bond 0.03098 / 2.01 ( 375) hydrogen bonds : angle 4.18165 / 3.07 ( 1100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.179 Fit side-chains REVERT: A 170 GLN cc_start: 0.8222 (tp40) cc_final: 0.7826 (tp-100) REVERT: A 263 LYS cc_start: 0.8220 (mmpt) cc_final: 0.8002 (mmmt) REVERT: A 276 MET cc_start: 0.6559 (mmm) cc_final: 0.6018 (mmt) REVERT: A 303 LEU cc_start: 0.8810 (mt) cc_final: 0.8591 (mp) REVERT: B 105 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6466 (tt0) REVERT: B 155 SER cc_start: 0.8805 (p) cc_final: 0.8304 (t) REVERT: B 200 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6864 (pt) REVERT: C 81 ILE cc_start: 0.8390 (mm) cc_final: 0.8066 (mm) REVERT: C 95 TRP cc_start: 0.7643 (p-90) cc_final: 0.7369 (p-90) outliers start: 18 outliers final: 14 residues processed: 114 average time/residue: 0.0788 time to fit residues: 12.0016 Evaluate side-chains 116 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 chunk 80 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 0.0170 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 45 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144260 restraints weight = 18326.124| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.79 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7044 Z= 0.116 Angle : 0.570 7.836 9579 Z= 0.276 Chirality : 0.039 0.133 1140 Planarity : 0.005 0.062 1132 Dihedral : 10.066 58.665 1139 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.96 % Allowed : 15.11 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.29), residues: 865 helix: 2.00 (0.26), residues: 383 sheet: -0.91 (0.37), residues: 199 loop : -2.30 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 40 TYR 0.010 0.001 TYR A 251 PHE 0.018 0.001 PHE A 298 TRP 0.014 0.001 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7040) covalent geometry : angle 0.56988 / 0.28 ( 9571) SS BOND : bond 0.00258 / 0.13 ( 4) SS BOND : angle 0.77606 / 0.42 ( 8) hydrogen bonds : bond 0.03125 / 2.04 ( 375) hydrogen bonds : angle 4.14126 / 3.04 ( 1100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.234 Fit side-chains REVERT: A 170 GLN cc_start: 0.8246 (tp40) cc_final: 0.7847 (tp-100) REVERT: A 263 LYS cc_start: 0.8178 (mmpt) cc_final: 0.7973 (mmmt) REVERT: A 276 MET cc_start: 0.6500 (mmm) cc_final: 0.5953 (mmt) REVERT: A 303 LEU cc_start: 0.8797 (mt) cc_final: 0.8505 (mp) REVERT: B 105 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6465 (tt0) REVERT: B 155 SER cc_start: 0.8785 (p) cc_final: 0.8317 (t) REVERT: B 200 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6768 (pt) REVERT: C 81 ILE cc_start: 0.8384 (mm) cc_final: 0.8075 (mm) REVERT: C 95 TRP cc_start: 0.7793 (p-90) cc_final: 0.7499 (p-90) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 0.0786 time to fit residues: 11.8641 Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.174493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139604 restraints weight = 24624.648| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 4.98 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7044 Z= 0.173 Angle : 0.629 8.000 9579 Z= 0.306 Chirality : 0.041 0.137 1140 Planarity : 0.005 0.063 1132 Dihedral : 10.157 58.728 1139 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.12 % Allowed : 14.78 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.29), residues: 865 helix: 1.90 (0.26), residues: 382 sheet: -0.82 (0.37), residues: 202 loop : -2.37 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.013 0.001 TYR A 141 PHE 0.021 0.002 PHE B 89 TRP 0.016 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 7040) covalent geometry : angle 0.62868 / 0.31 ( 9571) SS BOND : bond 0.00239 / 0.12 ( 4) SS BOND : angle 0.83629 / 0.46 ( 8) hydrogen bonds : bond 0.03444 / 2.24 ( 375) hydrogen bonds : angle 4.33103 / 3.16 ( 1100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.222 Fit side-chains REVERT: A 103 TRP cc_start: 0.7646 (t-100) cc_final: 0.7381 (t60) REVERT: A 170 GLN cc_start: 0.8308 (tp40) cc_final: 0.7903 (tp-100) REVERT: A 263 LYS cc_start: 0.8231 (mmpt) cc_final: 0.8013 (mmmt) REVERT: A 276 MET cc_start: 0.6536 (mmm) cc_final: 0.5980 (mmt) REVERT: B 105 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6247 (tm-30) REVERT: B 155 SER cc_start: 0.8817 (p) cc_final: 0.8325 (t) REVERT: B 200 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6730 (pt) REVERT: C 81 ILE cc_start: 0.8417 (mm) cc_final: 0.8069 (mm) REVERT: C 95 TRP cc_start: 0.7775 (p-90) cc_final: 0.7477 (p-90) outliers start: 19 outliers final: 17 residues processed: 108 average time/residue: 0.0775 time to fit residues: 11.2362 Evaluate side-chains 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 82 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140599 restraints weight = 24721.296| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 4.83 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7044 Z= 0.156 Angle : 0.617 7.555 9579 Z= 0.299 Chirality : 0.041 0.135 1140 Planarity : 0.005 0.063 1132 Dihedral : 10.018 59.114 1139 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.79 % Allowed : 15.27 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.29), residues: 865 helix: 1.92 (0.26), residues: 383 sheet: -0.86 (0.37), residues: 202 loop : -2.39 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.011 0.001 TYR A 251 PHE 0.018 0.001 PHE B 89 TRP 0.016 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 7040) covalent geometry : angle 0.61673 / 0.30 ( 9571) SS BOND : bond 0.00272 / 0.13 ( 4) SS BOND : angle 0.79158 / 0.43 ( 8) hydrogen bonds : bond 0.03356 / 2.18 ( 375) hydrogen bonds : angle 4.31691 / 3.16 ( 1100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 103 TRP cc_start: 0.7653 (t-100) cc_final: 0.7400 (t60) REVERT: A 170 GLN cc_start: 0.8263 (tp40) cc_final: 0.7833 (tp-100) REVERT: A 263 LYS cc_start: 0.8213 (mmpt) cc_final: 0.7989 (mmmt) REVERT: A 276 MET cc_start: 0.6539 (mmm) cc_final: 0.5991 (mmt) REVERT: A 303 LEU cc_start: 0.8862 (mt) cc_final: 0.8502 (mp) REVERT: B 105 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: B 155 SER cc_start: 0.8768 (p) cc_final: 0.8308 (t) REVERT: B 200 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6943 (pt) REVERT: C 81 ILE cc_start: 0.8464 (mm) cc_final: 0.8128 (mm) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.0853 time to fit residues: 12.3312 Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 52 optimal weight: 0.3980 chunk 79 optimal weight: 0.0030 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN ** A 311 ASN ** 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 = 0.4052 r_free = 0.4052 target = 0.177276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143321 restraints weight = 31819.471| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 5.58 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7044 Z= 0.133 Angle : 0.602 7.804 9579 Z= 0.291 Chirality : 0.040 0.135 1140 Planarity : 0.005 0.063 1132 Dihedral : 9.805 58.822 1139 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.96 % Allowed : 15.27 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.29), residues: 865 helix: 2.01 (0.26), residues: 383 sheet: -0.94 (0.37), residues: 205 loop : -2.36 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.011 0.001 TYR A 251 PHE 0.017 0.001 PHE A 298 TRP 0.015 0.001 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 7040) covalent geometry : angle 0.60210 / 0.29 ( 9571) SS BOND : bond 0.00245 / 0.12 ( 4) SS BOND : angle 0.72933 / 0.40 ( 8) hydrogen bonds : bond 0.03230 / 2.10 ( 375) hydrogen bonds : angle 4.23047 / 3.09 ( 1100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.64 seconds wall clock time: 23 minutes 56.14 seconds (1436.14 seconds total)