Starting phenix.real_space_refine on Wed Feb 12 21:08:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2u_27150/02_2025/8d2u_27150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2u_27150/02_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_27150/02_2025/8d2u_27150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2u_27150/02_2025/8d2u_27150.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2u_27150/02_2025/8d2u_27150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2u_27150/02_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-5592/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: 8.60, per 1000 atoms: 1.25 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: 2.00 Conformation dependent library (CDL) restraints added in 1.2 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: 0.68 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: 2.09 Time building geometry restraints manager: 2.26 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: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.980 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- 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 : 0.625 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: 0.1940 time to fit residues: 37.7831 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 : 0.702 ------------------------------------------------------------------------------- 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 = 19901.811| |-----------------------------------------------------------------------------| 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 : 0.638 Fit side-chains REVERT: A 103 TRP cc_start: 0.8343 (t-100) cc_final: 0.8051 (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: 0.2186 time to fit residues: 32.3145 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 : 0.675 ------------------------------------------------------------------------------- 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: 0.1980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.175624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137603 restraints weight = 23145.803| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 5.17 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7040 Z= 0.220 Angle : 0.665 7.647 9571 Z= 0.310 Chirality : 0.042 0.239 1140 Planarity : 0.005 0.060 1132 Dihedral : 12.720 59.699 1805 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: -0.66 (0.28), residues: 865 helix: 1.31 (0.26), residues: 383 sheet: -1.13 (0.36), residues: 199 loop : -2.36 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 140 HIS 0.002 0.001 HIS A 156 PHE 0.019 0.002 PHE A 298 TYR 0.012 0.001 TYR A 251 ARG 0.003 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 : 0.643 Fit side-chains REVERT: A 276 MET cc_start: 0.6586 (mmm) cc_final: 0.6080 (mmt) REVERT: A 411 LYS cc_start: 0.8390 (tmmt) cc_final: 0.8064 (tmtt) REVERT: B 91 LYS cc_start: 0.8333 (mttt) cc_final: 0.8085 (mtpt) REVERT: B 105 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6252 (tm-30) REVERT: C 81 ILE cc_start: 0.8410 (mm) cc_final: 0.8074 (mm) REVERT: C 95 TRP cc_start: 0.7767 (p-90) cc_final: 0.7347 (p-90) outliers start: 13 outliers final: 9 residues processed: 114 average time/residue: 0.2071 time to fit residues: 30.9324 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 : 0.675 ------------------------------------------------------------------------------- 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: 0.0570 chunk 70 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.172640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145099 restraints weight = 27901.574| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.70 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 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 = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7040 Z= 0.247 Angle : 0.641 7.473 9571 Z= 0.307 Chirality : 0.043 0.291 1140 Planarity : 0.005 0.064 1132 Dihedral : 11.548 59.979 1805 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.79 % Allowed : 14.12 % Favored : 83.09 % 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: -0.49 (0.29), residues: 865 helix: 1.46 (0.26), residues: 386 sheet: -1.05 (0.37), residues: 197 loop : -2.31 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 103 HIS 0.003 0.001 HIS A 156 PHE 0.018 0.002 PHE B 89 TYR 0.012 0.001 TYR A 251 ARG 0.002 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 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.716 Fit side-chains REVERT: A 103 TRP cc_start: 0.7426 (t-100) cc_final: 0.7174 (t60) REVERT: A 170 GLN cc_start: 0.8426 (tp40) cc_final: 0.7953 (tp-100) REVERT: A 263 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7971 (mmmt) REVERT: A 276 MET cc_start: 0.6438 (mmm) cc_final: 0.5952 (mmt) REVERT: A 303 LEU cc_start: 0.8852 (mt) cc_final: 0.8608 (mp) REVERT: B 91 LYS cc_start: 0.8410 (mttt) cc_final: 0.8059 (mtpt) REVERT: B 105 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6041 (tm-30) REVERT: B 200 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.7029 (pt) REVERT: C 81 ILE cc_start: 0.8563 (mm) cc_final: 0.8209 (mm) REVERT: C 95 TRP cc_start: 0.7834 (p-90) cc_final: 0.7437 (p-90) outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.2004 time to fit residues: 32.0003 Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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 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 78 optimal weight: 0.0980 chunk 70 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 4 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.174853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143272 restraints weight = 16590.802| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.93 r_work: 0.3284 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7040 Z= 0.187 Angle : 0.593 6.608 9571 Z= 0.285 Chirality : 0.040 0.200 1140 Planarity : 0.005 0.063 1132 Dihedral : 10.932 59.967 1805 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.96 % Allowed : 14.94 % 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: -0.32 (0.29), residues: 865 helix: 1.62 (0.26), residues: 388 sheet: -0.95 (0.37), residues: 197 loop : -2.30 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 344 HIS 0.001 0.001 HIS A 156 PHE 0.015 0.001 PHE C 38 TYR 0.010 0.001 TYR A 251 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 123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.720 Fit side-chains REVERT: A 103 TRP cc_start: 0.7861 (t-100) cc_final: 0.7554 (t60) REVERT: A 170 GLN cc_start: 0.8318 (tp40) cc_final: 0.7888 (tp-100) REVERT: A 263 LYS cc_start: 0.8306 (mmpt) cc_final: 0.7805 (mmpt) REVERT: A 276 MET cc_start: 0.6185 (mmm) cc_final: 0.5618 (mmt) REVERT: A 303 LEU cc_start: 0.8733 (mt) cc_final: 0.8448 (mp) REVERT: B 91 LYS cc_start: 0.8724 (mttt) cc_final: 0.8328 (mtpt) REVERT: B 105 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6686 (tt0) REVERT: B 200 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6563 (pt) REVERT: C 81 ILE cc_start: 0.8455 (mm) cc_final: 0.8153 (mm) REVERT: C 95 TRP cc_start: 0.8280 (p-90) cc_final: 0.7759 (p-90) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.2068 time to fit residues: 31.5396 Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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 13 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.171557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134567 restraints weight = 27067.961| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 5.50 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7040 Z= 0.296 Angle : 0.641 8.133 9571 Z= 0.311 Chirality : 0.042 0.204 1140 Planarity : 0.005 0.067 1132 Dihedral : 10.852 59.287 1805 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.61 % Allowed : 14.45 % 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: -0.41 (0.29), residues: 865 helix: 1.57 (0.26), residues: 385 sheet: -1.00 (0.37), residues: 197 loop : -2.34 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.022 0.002 PHE B 89 TYR 0.013 0.001 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 123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.904 Fit side-chains REVERT: A 263 LYS cc_start: 0.8288 (mmpt) cc_final: 0.7871 (mmpt) REVERT: A 276 MET cc_start: 0.6567 (mmm) cc_final: 0.6032 (mmt) REVERT: A 303 LEU cc_start: 0.8869 (mt) cc_final: 0.8554 (mp) REVERT: B 105 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: B 200 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7028 (pt) REVERT: C 81 ILE cc_start: 0.8531 (mm) cc_final: 0.8183 (mm) REVERT: C 95 TRP cc_start: 0.7870 (p-90) cc_final: 0.7591 (p-90) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.2134 time to fit residues: 32.1147 Evaluate side-chains 111 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.171724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133386 restraints weight = 20684.969| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 5.17 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2958 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= 0.243 Angle : 0.618 7.448 9571 Z= 0.297 Chirality : 0.041 0.219 1140 Planarity : 0.005 0.067 1132 Dihedral : 10.563 57.943 1805 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % 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 (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: 1.71 (0.26), residues: 382 sheet: -0.93 (0.37), residues: 197 loop : -2.33 (0.34), residues: 286 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 0.020 0.001 PHE B 89 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 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.654 Fit side-chains REVERT: A 170 GLN cc_start: 0.8219 (tp40) cc_final: 0.7812 (tp-100) REVERT: A 263 LYS cc_start: 0.8303 (mmpt) cc_final: 0.7885 (mmpt) REVERT: A 276 MET cc_start: 0.6620 (mmm) cc_final: 0.6063 (mmt) REVERT: A 303 LEU cc_start: 0.8813 (mt) cc_final: 0.8479 (mp) REVERT: B 105 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6514 (tt0) REVERT: B 200 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6906 (pt) REVERT: C 81 ILE cc_start: 0.8384 (mm) cc_final: 0.8019 (mm) REVERT: C 95 TRP cc_start: 0.7911 (p-90) cc_final: 0.7588 (p-90) outliers start: 18 outliers final: 14 residues processed: 109 average time/residue: 0.2244 time to fit residues: 31.9099 Evaluate side-chains 114 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.3980 chunk 51 optimal weight: 0.0670 chunk 58 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.170171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133124 restraints weight = 24885.619| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 5.26 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7040 Z= 0.322 Angle : 0.660 8.598 9571 Z= 0.322 Chirality : 0.043 0.297 1140 Planarity : 0.005 0.069 1132 Dihedral : 10.440 58.022 1805 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % 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: -0.45 (0.29), residues: 865 helix: 1.56 (0.26), residues: 385 sheet: -1.03 (0.36), residues: 202 loop : -2.41 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.024 0.002 PHE B 89 TYR 0.013 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 113 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.729 Fit side-chains REVERT: A 170 GLN cc_start: 0.8295 (tp40) cc_final: 0.7906 (tp-100) REVERT: A 263 LYS cc_start: 0.8343 (mmpt) cc_final: 0.7996 (mmpt) REVERT: A 276 MET cc_start: 0.6536 (mmm) cc_final: 0.6002 (mmt) REVERT: A 303 LEU cc_start: 0.8923 (mt) cc_final: 0.8581 (mp) REVERT: B 105 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6568 (tt0) REVERT: B 200 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7082 (pt) REVERT: C 81 ILE cc_start: 0.8501 (mm) cc_final: 0.8141 (mm) REVERT: C 95 TRP cc_start: 0.7875 (p-90) cc_final: 0.7572 (p-90) outliers start: 19 outliers final: 15 residues processed: 103 average time/residue: 0.2083 time to fit residues: 28.2142 Evaluate side-chains 112 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 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 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.171151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133147 restraints weight = 28772.723| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 6.01 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7040 Z= 0.264 Angle : 0.634 7.989 9571 Z= 0.309 Chirality : 0.041 0.233 1140 Planarity : 0.005 0.069 1132 Dihedral : 10.213 58.622 1805 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.96 % Allowed : 14.94 % 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: -0.37 (0.29), residues: 865 helix: 1.70 (0.26), residues: 383 sheet: -1.06 (0.36), residues: 201 loop : -2.40 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.019 0.001 PHE B 89 TYR 0.011 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 112 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.770 Fit side-chains REVERT: A 170 GLN cc_start: 0.8292 (tp40) cc_final: 0.7893 (tp-100) REVERT: A 263 LYS cc_start: 0.8339 (mmpt) cc_final: 0.8003 (mmpt) REVERT: A 276 MET cc_start: 0.6620 (mmm) cc_final: 0.6065 (mmt) REVERT: A 303 LEU cc_start: 0.8903 (mt) cc_final: 0.8576 (mp) REVERT: B 105 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6521 (tt0) REVERT: B 155 SER cc_start: 0.8698 (p) cc_final: 0.8205 (t) REVERT: B 200 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7072 (pt) REVERT: C 81 ILE cc_start: 0.8505 (mm) cc_final: 0.8146 (mm) REVERT: C 95 TRP cc_start: 0.7833 (p-90) cc_final: 0.7559 (p-90) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.2310 time to fit residues: 30.7798 Evaluate side-chains 111 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 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 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 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 57 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.173924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135371 restraints weight = 22290.785| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 5.08 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7040 Z= 0.197 Angle : 0.592 7.490 9571 Z= 0.287 Chirality : 0.039 0.173 1140 Planarity : 0.005 0.069 1132 Dihedral : 9.829 59.676 1805 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.30 % Allowed : 15.76 % 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: -0.20 (0.29), residues: 865 helix: 1.88 (0.26), residues: 385 sheet: -0.98 (0.36), residues: 202 loop : -2.39 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.015 0.001 PHE C 38 TYR 0.011 0.001 TYR A 251 ARG 0.001 0.000 ARG A 108 ********************** 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 108 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.593 Fit side-chains REVERT: A 170 GLN cc_start: 0.8269 (tp40) cc_final: 0.7820 (tp-100) REVERT: A 263 LYS cc_start: 0.8307 (mmpt) cc_final: 0.8023 (mmpt) REVERT: A 276 MET cc_start: 0.6580 (mmm) cc_final: 0.6034 (mmt) REVERT: A 303 LEU cc_start: 0.8790 (mt) cc_final: 0.8438 (mp) REVERT: B 105 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6384 (tt0) REVERT: B 155 SER cc_start: 0.8637 (p) cc_final: 0.8233 (t) REVERT: B 200 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7015 (pt) REVERT: C 81 ILE cc_start: 0.8467 (mm) cc_final: 0.8132 (mm) REVERT: C 95 TRP cc_start: 0.7830 (p-90) cc_final: 0.7519 (p-90) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.2183 time to fit residues: 28.6606 Evaluate side-chains 108 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.172050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135007 restraints weight = 23150.016| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 5.14 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7040 Z= 0.229 Angle : 0.604 7.589 9571 Z= 0.293 Chirality : 0.040 0.206 1140 Planarity : 0.005 0.068 1132 Dihedral : 9.848 59.844 1805 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.46 % Allowed : 15.76 % 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 (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: -0.18 (0.29), residues: 865 helix: 1.93 (0.26), residues: 383 sheet: -0.98 (0.36), residues: 202 loop : -2.40 (0.34), residues: 280 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 0.017 0.001 PHE B 89 TYR 0.011 0.001 TYR A 251 ARG 0.001 0.000 ARG A 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.64 seconds wall clock time: 56 minutes 3.53 seconds (3363.53 seconds total)