Starting phenix.real_space_refine on Wed Mar 12 22:03:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2u_27150/03_2025/8d2u_27150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2u_27150/03_2025/8d2u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2u_27150/03_2025/8d2u_27150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2u_27150/03_2025/8d2u_27150.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2u_27150/03_2025/8d2u_27150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2u_27150/03_2025/8d2u_27150.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} 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: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2, '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: 210 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: 210 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: 7.23, per 1000 atoms: 1.05 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.70 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: 2.05 Time building geometry restraints manager: 2.20 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 - 23.52: 4087 23.52 - 47.03: 262 47.03 - 70.55: 99 70.55 - 94.07: 56 94.07 - 117.58: 96 Dihedral angle restraints: 4600 sinusoidal: 2136 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=" C5B LMT A 604 " pdb=" C1B LMT A 604 " pdb=" O5B LMT A 604 " pdb=" O1B LMT A 604 " ideal model delta sinusoidal sigma weight residual 295.61 178.03 117.58 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C2B LMT A 604 " pdb=" C1B LMT A 604 " pdb=" O5B LMT A 604 " pdb=" C5B LMT A 604 " ideal model delta sinusoidal sigma weight residual -57.12 59.92 -117.04 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 4597 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: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 7040 Z= 0.771 Angle : 1.445 29.303 9571 Z= 0.602 Chirality : 0.054 0.300 1140 Planarity : 0.007 0.067 1132 Dihedral : 27.080 117.582 3018 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (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 TRP 0.015 0.002 TRP A 140 HIS 0.003 0.001 HIS A 156 PHE 0.031 0.002 PHE C 38 TYR 0.017 0.002 TYR A 50 ARG 0.001 0.000 ARG C 92 *********************** 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 : 0.664 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: 0.2420 time to fit residues: 47.0421 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 : 0.687 ------------------------------------------------------------------------------- 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 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 78 optimal weight: 0.9980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4058 r_free = 0.4058 target = 0.179247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142610 restraints weight = 19901.808| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 4.50 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7040 Z= 0.209 Angle : 0.806 9.522 9571 Z= 0.351 Chirality : 0.048 0.264 1140 Planarity : 0.006 0.058 1132 Dihedral : 18.893 78.201 1806 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.48 % Allowed : 13.79 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.27), residues: 865 helix: 0.65 (0.25), residues: 386 sheet: -1.17 (0.35), residues: 198 loop : -2.39 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 103 HIS 0.002 0.001 HIS A 420 PHE 0.017 0.002 PHE A 427 TYR 0.009 0.001 TYR A 251 ARG 0.005 0.001 ARG A 108 *********************** 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 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.683 Fit side-chains REVERT: A 103 TRP cc_start: 0.8343 (t-100) cc_final: 0.8052 (t60) REVERT: A 108 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7314 (mtp180) REVERT: A 276 MET cc_start: 0.6415 (mmm) cc_final: 0.6025 (mmt) REVERT: A 411 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7900 (tmtt) REVERT: B 91 LYS cc_start: 0.8284 (mttt) cc_final: 0.8080 (mtpt) REVERT: C 81 ILE cc_start: 0.8418 (mm) cc_final: 0.8109 (mm) REVERT: C 95 TRP cc_start: 0.7451 (p-90) cc_final: 0.7197 (p-90) outliers start: 9 outliers final: 3 residues processed: 113 average time/residue: 0.2408 time to fit residues: 35.7348 Evaluate side-chains 102 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR 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 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.0040 chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137426 restraints weight = 23167.193| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 5.10 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7040 Z= 0.234 Angle : 0.672 8.242 9571 Z= 0.314 Chirality : 0.043 0.250 1140 Planarity : 0.005 0.061 1132 Dihedral : 12.752 59.894 1805 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.13 % Allowed : 14.12 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 865 helix: 1.30 (0.26), residues: 383 sheet: -1.14 (0.36), residues: 199 loop : -2.36 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 140 HIS 0.002 0.001 HIS A 156 PHE 0.018 0.002 PHE B 89 TYR 0.013 0.001 TYR A 251 ARG 0.002 0.000 ARG A 455 *********************** 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 122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.661 Fit side-chains REVERT: A 276 MET cc_start: 0.6563 (mmm) cc_final: 0.6061 (mmt) REVERT: A 411 LYS cc_start: 0.8361 (tmmt) cc_final: 0.8042 (tmtt) REVERT: B 91 LYS cc_start: 0.8337 (mttt) cc_final: 0.8082 (mtpt) REVERT: B 105 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6313 (tm-30) REVERT: C 81 ILE cc_start: 0.8451 (mm) cc_final: 0.8119 (mm) REVERT: C 95 TRP cc_start: 0.7748 (p-90) cc_final: 0.7363 (p-90) outliers start: 13 outliers final: 9 residues processed: 114 average time/residue: 0.2650 time to fit residues: 39.7210 Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP 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 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 53 optimal weight: 0.3980 chunk 70 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3988 r_free = 0.3988 target = 0.174465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149534 restraints weight = 27835.846| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.32 r_work: 0.3190 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7040 Z= 0.211 Angle : 0.617 6.601 9571 Z= 0.294 Chirality : 0.042 0.279 1140 Planarity : 0.005 0.063 1132 Dihedral : 11.538 59.724 1805 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.30 % Allowed : 14.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.29), residues: 865 helix: 1.49 (0.26), residues: 388 sheet: -1.01 (0.37), residues: 197 loop : -2.30 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 103 HIS 0.002 0.001 HIS A 156 PHE 0.018 0.001 PHE A 298 TYR 0.012 0.001 TYR A 251 ARG 0.001 0.000 ARG A 455 *********************** 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 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.723 Fit side-chains REVERT: A 103 TRP cc_start: 0.7924 (t-100) cc_final: 0.7622 (t60) REVERT: A 170 GLN cc_start: 0.8254 (tp40) cc_final: 0.7828 (tp-100) REVERT: A 263 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7759 (mmpt) REVERT: A 276 MET cc_start: 0.6231 (mmm) cc_final: 0.5662 (mmt) REVERT: A 303 LEU cc_start: 0.8848 (mt) cc_final: 0.8476 (mp) REVERT: A 411 LYS cc_start: 0.8771 (tmmt) cc_final: 0.8515 (tmtt) REVERT: B 91 LYS cc_start: 0.8766 (mttt) cc_final: 0.8376 (mtpt) REVERT: B 105 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6160 (tm-30) REVERT: B 200 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6663 (pt) REVERT: C 81 ILE cc_start: 0.8491 (mm) cc_final: 0.8172 (mm) REVERT: C 95 TRP cc_start: 0.8349 (p-90) cc_final: 0.7811 (p-90) outliers start: 14 outliers final: 9 residues processed: 115 average time/residue: 0.2131 time to fit residues: 33.1855 Evaluate side-chains 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE 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 B residue 200 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 90 THR 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 78 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 37 optimal weight: 0.0670 chunk 4 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.175747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143682 restraints weight = 16695.355| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.05 r_work: 0.3286 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7040 Z= 0.169 Angle : 0.576 6.584 9571 Z= 0.276 Chirality : 0.039 0.194 1140 Planarity : 0.005 0.061 1132 Dihedral : 10.733 59.410 1805 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.96 % Allowed : 14.61 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 865 helix: 1.74 (0.26), residues: 386 sheet: -1.09 (0.37), residues: 199 loop : -2.28 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.001 0.000 HIS A 156 PHE 0.015 0.001 PHE C 38 TYR 0.010 0.001 TYR A 428 ARG 0.001 0.000 ARG A 455 *********************** 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 125 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.680 Fit side-chains REVERT: A 103 TRP cc_start: 0.7886 (t-100) cc_final: 0.7671 (t60) REVERT: A 170 GLN cc_start: 0.8288 (tp40) cc_final: 0.7850 (tp-100) REVERT: A 263 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7802 (mmpt) REVERT: A 276 MET cc_start: 0.6186 (mmm) cc_final: 0.5610 (mmt) REVERT: A 303 LEU cc_start: 0.8725 (mt) cc_final: 0.8453 (mp) REVERT: A 411 LYS cc_start: 0.8838 (tmmt) cc_final: 0.8626 (tmtt) REVERT: B 91 LYS cc_start: 0.8694 (mttt) cc_final: 0.8298 (mtpt) REVERT: B 105 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: B 168 MET cc_start: 0.8568 (ttm) cc_final: 0.8141 (ttt) REVERT: B 200 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6554 (pt) REVERT: C 81 ILE cc_start: 0.8383 (mm) cc_final: 0.8081 (mm) REVERT: C 95 TRP cc_start: 0.8234 (p-90) cc_final: 0.7727 (p-90) outliers start: 18 outliers final: 11 residues processed: 114 average time/residue: 0.1975 time to fit residues: 30.0770 Evaluate side-chains 116 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 163 SER 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 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3953 r_free = 0.3953 target = 0.171418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143059 restraints weight = 26601.039| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.67 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7040 Z= 0.285 Angle : 0.638 8.008 9571 Z= 0.310 Chirality : 0.042 0.203 1140 Planarity : 0.005 0.065 1132 Dihedral : 10.744 58.464 1805 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.61 % Allowed : 14.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 865 helix: 1.62 (0.26), residues: 385 sheet: -0.99 (0.37), residues: 197 loop : -2.31 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 140 HIS 0.003 0.001 HIS A 156 PHE 0.023 0.002 PHE B 89 TYR 0.013 0.002 TYR A 141 ARG 0.002 0.000 ARG A 455 *********************** 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 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.734 Fit side-chains REVERT: A 263 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7795 (mmpt) REVERT: A 276 MET cc_start: 0.6384 (mmm) cc_final: 0.5875 (mmt) REVERT: A 303 LEU cc_start: 0.8820 (mt) cc_final: 0.8479 (mp) REVERT: B 91 LYS cc_start: 0.8382 (mttt) cc_final: 0.8050 (mtpt) REVERT: B 105 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6078 (tm-30) REVERT: B 200 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6950 (pt) REVERT: C 23 LYS cc_start: 0.8092 (tttm) cc_final: 0.7866 (mtpt) REVERT: C 81 ILE cc_start: 0.8425 (mm) cc_final: 0.8067 (mm) REVERT: C 95 TRP cc_start: 0.7900 (p-90) cc_final: 0.7520 (p-90) outliers start: 22 outliers final: 16 residues processed: 120 average time/residue: 0.2125 time to fit residues: 33.2291 Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 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 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 7 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 63 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN C 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141592 restraints weight = 20369.108| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.57 r_work: 0.3168 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7040 Z= 0.246 Angle : 0.619 7.404 9571 Z= 0.299 Chirality : 0.041 0.229 1140 Planarity : 0.005 0.065 1132 Dihedral : 10.525 57.730 1805 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.29), residues: 865 helix: 1.72 (0.26), residues: 382 sheet: -0.95 (0.37), residues: 202 loop : -2.35 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.019 0.001 PHE A 298 TYR 0.011 0.001 TYR A 251 ARG 0.001 0.000 ARG A 455 *********************** 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 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.881 Fit side-chains REVERT: A 170 GLN cc_start: 0.8110 (tp40) cc_final: 0.7800 (tp-100) REVERT: A 263 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7870 (mmpt) REVERT: A 276 MET cc_start: 0.6185 (mmm) cc_final: 0.5601 (mmt) REVERT: A 303 LEU cc_start: 0.8807 (mt) cc_final: 0.8489 (mp) REVERT: B 91 LYS cc_start: 0.8790 (mttt) cc_final: 0.8376 (mtpt) REVERT: B 105 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6754 (tt0) REVERT: B 200 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6695 (pt) REVERT: C 23 LYS cc_start: 0.8300 (tttm) cc_final: 0.8029 (mtpt) REVERT: C 81 ILE cc_start: 0.8402 (mm) cc_final: 0.8068 (mm) REVERT: C 95 TRP cc_start: 0.8419 (p-90) cc_final: 0.7894 (p-90) outliers start: 19 outliers final: 15 residues processed: 111 average time/residue: 0.2175 time to fit residues: 32.0151 Evaluate side-chains 116 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 58 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.169163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132180 restraints weight = 24817.019| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 5.18 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 7040 Z= 0.378 Angle : 0.694 9.364 9571 Z= 0.340 Chirality : 0.044 0.332 1140 Planarity : 0.005 0.068 1132 Dihedral : 10.695 58.014 1805 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.29), residues: 865 helix: 1.46 (0.26), residues: 385 sheet: -1.10 (0.36), residues: 201 loop : -2.45 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.026 0.002 PHE B 89 TYR 0.016 0.002 TYR A 141 ARG 0.002 0.000 ARG A 455 *********************** 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 114 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.723 Fit side-chains REVERT: A 263 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7976 (mmpt) REVERT: A 276 MET cc_start: 0.6513 (mmm) cc_final: 0.5975 (mmt) REVERT: A 303 LEU cc_start: 0.8945 (mt) cc_final: 0.8627 (mp) REVERT: B 91 LYS cc_start: 0.8381 (mttt) cc_final: 0.8115 (mtpt) REVERT: B 105 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6633 (tt0) REVERT: B 200 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6971 (pt) REVERT: C 81 ILE cc_start: 0.8547 (mm) cc_final: 0.8170 (mm) REVERT: C 95 TRP cc_start: 0.7800 (p-90) cc_final: 0.7447 (p-90) outliers start: 17 outliers final: 13 residues processed: 106 average time/residue: 0.2251 time to fit residues: 30.8138 Evaluate side-chains 113 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 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 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.0020 chunk 76 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135757 restraints weight = 28852.385| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 6.10 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7040 Z= 0.183 Angle : 0.596 8.056 9571 Z= 0.289 Chirality : 0.040 0.171 1140 Planarity : 0.005 0.067 1132 Dihedral : 10.165 58.730 1805 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.30 % Allowed : 15.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 865 helix: 1.78 (0.26), residues: 385 sheet: -1.07 (0.36), residues: 204 loop : -2.35 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 344 HIS 0.002 0.001 HIS A 288 PHE 0.019 0.001 PHE A 298 TYR 0.010 0.001 TYR A 251 ARG 0.001 0.000 ARG A 455 *********************** 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 107 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.729 Fit side-chains REVERT: A 170 GLN cc_start: 0.8208 (tp40) cc_final: 0.7806 (tp-100) REVERT: A 263 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8002 (mmpt) REVERT: A 276 MET cc_start: 0.6661 (mmm) cc_final: 0.6097 (mmt) REVERT: A 303 LEU cc_start: 0.8830 (mt) cc_final: 0.8512 (mp) REVERT: B 91 LYS cc_start: 0.8337 (mttt) cc_final: 0.8041 (mtpt) REVERT: B 105 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6254 (tt0) REVERT: B 155 SER cc_start: 0.8762 (p) cc_final: 0.8283 (t) REVERT: B 200 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7009 (pt) REVERT: C 81 ILE cc_start: 0.8407 (mm) cc_final: 0.8054 (mm) REVERT: C 95 TRP cc_start: 0.7793 (p-90) cc_final: 0.7505 (p-90) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.2229 time to fit residues: 29.6376 Evaluate side-chains 107 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 75 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.0570 chunk 21 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137182 restraints weight = 22240.025| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.96 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7040 Z= 0.170 Angle : 0.577 7.647 9571 Z= 0.278 Chirality : 0.039 0.165 1140 Planarity : 0.005 0.066 1132 Dihedral : 9.809 59.837 1805 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.46 % Allowed : 15.11 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 865 helix: 2.03 (0.26), residues: 383 sheet: -0.97 (0.36), residues: 205 loop : -2.32 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.002 0.001 HIS A 288 PHE 0.016 0.001 PHE A 298 TYR 0.010 0.001 TYR A 251 ARG 0.001 0.000 ARG A 455 ********************** 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 115 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.714 Fit side-chains REVERT: A 170 GLN cc_start: 0.8228 (tp40) cc_final: 0.7891 (tp-100) REVERT: A 263 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7944 (mmpt) REVERT: A 276 MET cc_start: 0.6560 (mmm) cc_final: 0.6006 (mmt) REVERT: A 303 LEU cc_start: 0.8743 (mt) cc_final: 0.8387 (mp) REVERT: B 91 LYS cc_start: 0.8245 (mttt) cc_final: 0.7969 (mtpt) REVERT: B 105 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6138 (tt0) REVERT: B 155 SER cc_start: 0.8797 (p) cc_final: 0.8411 (t) REVERT: B 200 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6978 (pt) REVERT: C 81 ILE cc_start: 0.8453 (mm) cc_final: 0.8155 (mm) REVERT: C 95 TRP cc_start: 0.7795 (p-90) cc_final: 0.7498 (p-90) outliers start: 15 outliers final: 12 residues processed: 107 average time/residue: 0.2252 time to fit residues: 31.9622 Evaluate side-chains 112 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 348 LEU 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 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 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 31 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.171275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134416 restraints weight = 23154.824| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 5.04 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7040 Z= 0.257 Angle : 0.616 7.538 9571 Z= 0.301 Chirality : 0.041 0.225 1140 Planarity : 0.005 0.066 1132 Dihedral : 9.976 59.687 1805 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.46 % Allowed : 16.09 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.29), residues: 865 helix: 1.96 (0.26), residues: 382 sheet: -1.03 (0.36), residues: 205 loop : -2.40 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.019 0.001 PHE B 89 TYR 0.012 0.001 TYR A 251 ARG 0.002 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3966.51 seconds wall clock time: 72 minutes 22.50 seconds (4342.50 seconds total)