Starting phenix.real_space_refine on Wed Feb 14 02:50:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2u_27150/02_2024/8d2u_27150_updated.pdb" } 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 Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.07, per 1000 atoms: 0.88 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 - 3.50 Amino acid : False - 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: 2.54 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 18 helices and 10 sheets defined 41.1% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.835A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Proline residue: A 49 - end of helix 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 73 through 99 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 110 through 127 Proline residue: A 118 - end of helix removed outlier: 3.630A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 166 Proline residue: A 158 - end of helix removed outlier: 4.301A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 199 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 233 through 261 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 289 through 318 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 326 through 339 Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.862A pdb=" N THR A 349 " --> pdb=" O AGLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.922A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 413 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 420 through 450 removed outlier: 3.851A pdb=" N SER A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 493 through 506 removed outlier: 4.118A pdb=" N ARG A 496 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLY A 498 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing sheet with id= A, first strand: chain 'B' and resid 18 through 23 Processing sheet with id= B, first strand: chain 'B' and resid 83 through 88 removed outlier: 6.011A pdb=" N ASN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU B 45 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= D, first strand: chain 'B' and resid 140 through 144 Processing sheet with id= E, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= F, first strand: chain 'C' and resid 56 through 58 removed outlier: 7.102A pdb=" N TRP C 36 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA C 49 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 34 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 89 through 91 Processing sheet with id= H, 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= I, 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) Processing sheet with id= J, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.615A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 953 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: 1.87 Time building geometry restraints manager: 2.68 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: 98.79 - 110.32: 2018 110.32 - 121.86: 6161 121.86 - 133.39: 1365 133.39 - 144.93: 25 144.93 - 156.46: 2 Bond angle restraints: 9571 Sorted by residual: angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 109.50 132.09 -22.59 3.00e+00 1.11e-01 5.67e+01 angle pdb=" N ARG A 455 " pdb=" CA ARG A 455 " pdb=" C ARG A 455 " ideal model delta sigma weight residual 110.80 100.13 10.67 2.13e+00 2.20e-01 2.51e+01 angle pdb=" N THR C 151 " pdb=" CA THR C 151 " pdb=" C THR C 151 " ideal model delta sigma weight residual 109.24 115.93 -6.69 1.51e+00 4.39e-01 1.96e+01 angle pdb=" C10 ZGS A 601 " pdb=" C11 ZGS A 601 " pdb=" C12 ZGS A 601 " ideal model delta sigma weight residual 109.48 122.76 -13.28 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " pdb=" C09 ZGS A 601 " ideal model delta sigma weight residual 109.49 121.85 -12.36 3.00e+00 1.11e-01 1.70e+01 ... (remaining 9566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 4233 34.07 - 68.13: 202 68.13 - 102.20: 97 102.20 - 136.26: 53 136.26 - 170.33: 1 Dihedral angle restraints: 4586 sinusoidal: 2122 harmonic: 2464 Sorted by residual: dihedral pdb=" C23 ZGS A 601 " pdb=" C21 ZGS A 601 " pdb=" C22 ZGS A 601 " pdb=" O20 ZGS A 601 " ideal model delta sinusoidal sigma weight residual -159.35 10.98 -170.33 1 3.00e+01 1.11e-03 2.12e+01 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 ... (remaining 4583 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: 2323 2.85 - 3.37: 6013 3.37 - 3.88: 11565 3.88 - 4.39: 12770 4.39 - 4.90: 22547 Nonbonded interactions: 55218 Sorted by model distance: nonbonded pdb=" O TYR A 43 " pdb=" OH TYR A 159 " model vdw 2.344 2.440 nonbonded pdb=" O THR A 381 " pdb=" OG SER A 385 " model vdw 2.347 2.440 nonbonded pdb=" O SER A 439 " pdb=" OG SER A 443 " model vdw 2.354 2.440 nonbonded pdb=" O SER A 132 " pdb=" O2B LMT A 607 " model vdw 2.362 2.440 nonbonded pdb=" OH TYR A 43 " pdb=" OG1 THR A 163 " model vdw 2.372 2.440 ... (remaining 55213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 11.190 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.710 Find NCS groups from input model: 0.200 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 41.360 ------------------------------------------------------------------------------- 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= 0.756 Angle : 1.349 22.588 9571 Z= 0.577 Chirality : 0.054 0.300 1140 Planarity : 0.007 0.067 1132 Dihedral : 27.138 170.330 3004 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 fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 0.629 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: 0.1964 time to fit residues: 37.9891 Evaluate side-chains 104 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 0.0070 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN 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 145 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7040 Z= 0.281 Angle : 0.826 9.513 9571 Z= 0.363 Chirality : 0.049 0.291 1140 Planarity : 0.006 0.061 1132 Dihedral : 18.124 153.776 1792 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.13 % Allowed : 14.29 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.27), residues: 865 helix: 0.57 (0.26), residues: 381 sheet: -1.22 (0.35), residues: 202 loop : -2.51 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 103 HIS 0.003 0.001 HIS A 156 PHE 0.021 0.002 PHE A 144 TYR 0.013 0.002 TYR A 251 ARG 0.003 0.000 ARG C 31 *********************** 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 121 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.631 Fit side-chains REVERT: A 103 TRP cc_start: 0.8430 (t-100) cc_final: 0.8177 (t60) REVERT: A 109 MET cc_start: 0.7688 (mmt) cc_final: 0.7392 (mmt) REVERT: A 276 MET cc_start: 0.6262 (mmm) cc_final: 0.5871 (mmt) REVERT: B 91 LYS cc_start: 0.8441 (mttt) cc_final: 0.8077 (mtpt) REVERT: B 105 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6361 (tm-30) REVERT: C 81 ILE cc_start: 0.8271 (mm) cc_final: 0.7942 (mm) REVERT: C 95 TRP cc_start: 0.7652 (p-90) cc_final: 0.7297 (p-90) outliers start: 13 outliers final: 7 residues processed: 117 average time/residue: 0.1921 time to fit residues: 30.0037 Evaluate side-chains 104 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 174 SER 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 43 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 152 GLN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7040 Z= 0.297 Angle : 0.691 8.341 9571 Z= 0.327 Chirality : 0.043 0.237 1140 Planarity : 0.005 0.064 1132 Dihedral : 13.281 139.479 1791 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.61 % Allowed : 13.63 % Favored : 82.76 % 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: -0.99 (0.28), residues: 865 helix: 1.00 (0.26), residues: 380 sheet: -1.26 (0.36), residues: 195 loop : -2.44 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 140 HIS 0.003 0.001 HIS A 156 PHE 0.022 0.002 PHE B 89 TYR 0.014 0.002 TYR A 251 ARG 0.001 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 121 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.652 Fit side-chains REVERT: A 103 TRP cc_start: 0.8482 (t-100) cc_final: 0.8182 (t-100) REVERT: A 276 MET cc_start: 0.6287 (mmm) cc_final: 0.5909 (mmt) REVERT: B 91 LYS cc_start: 0.8463 (mttt) cc_final: 0.8108 (mtpt) REVERT: B 105 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6480 (tm-30) REVERT: C 95 TRP cc_start: 0.7904 (p-90) cc_final: 0.7313 (p-90) outliers start: 22 outliers final: 16 residues processed: 115 average time/residue: 0.2067 time to fit residues: 31.2732 Evaluate side-chains 106 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 199 VAL 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 472 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 90 THR 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 77 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7040 Z= 0.229 Angle : 0.623 7.337 9571 Z= 0.297 Chirality : 0.041 0.255 1140 Planarity : 0.005 0.063 1132 Dihedral : 12.164 125.723 1791 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.46 % Allowed : 16.58 % Favored : 80.95 % 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: -0.69 (0.28), residues: 865 helix: 1.27 (0.27), residues: 382 sheet: -1.19 (0.36), residues: 194 loop : -2.28 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 140 HIS 0.002 0.001 HIS A 156 PHE 0.017 0.002 PHE B 89 TYR 0.011 0.001 TYR A 251 ARG 0.001 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.699 Fit side-chains REVERT: A 103 TRP cc_start: 0.8499 (t-100) cc_final: 0.8201 (t-100) REVERT: A 108 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7679 (mtp-110) REVERT: A 276 MET cc_start: 0.6353 (mmm) cc_final: 0.5930 (mmt) REVERT: A 303 LEU cc_start: 0.8779 (mt) cc_final: 0.8513 (mp) REVERT: B 91 LYS cc_start: 0.8407 (mttt) cc_final: 0.8061 (mtpt) REVERT: B 105 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: B 200 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6851 (pt) REVERT: C 81 ILE cc_start: 0.8288 (mm) cc_final: 0.7994 (mm) REVERT: C 95 TRP cc_start: 0.7864 (p-90) cc_final: 0.7344 (p-90) outliers start: 15 outliers final: 8 residues processed: 108 average time/residue: 0.2127 time to fit residues: 29.9958 Evaluate side-chains 107 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 69 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7040 Z= 0.237 Angle : 0.610 7.331 9571 Z= 0.293 Chirality : 0.040 0.201 1140 Planarity : 0.005 0.064 1132 Dihedral : 11.493 107.288 1791 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.12 % Allowed : 15.27 % Favored : 81.61 % 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: -0.61 (0.28), residues: 865 helix: 1.43 (0.27), residues: 379 sheet: -1.22 (0.36), residues: 201 loop : -2.31 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 140 HIS 0.002 0.001 HIS A 156 PHE 0.018 0.002 PHE C 38 TYR 0.011 0.001 TYR A 251 ARG 0.001 0.000 ARG C 40 *********************** 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 117 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.684 Fit side-chains REVERT: A 103 TRP cc_start: 0.8473 (t-100) cc_final: 0.8190 (t-100) REVERT: A 263 LYS cc_start: 0.8350 (mmpt) cc_final: 0.8025 (mmmt) REVERT: A 276 MET cc_start: 0.6358 (mmm) cc_final: 0.5922 (mmt) REVERT: A 303 LEU cc_start: 0.8781 (mt) cc_final: 0.8513 (mp) REVERT: B 91 LYS cc_start: 0.8413 (mttt) cc_final: 0.8060 (mtpt) REVERT: B 105 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6162 (tm-30) REVERT: B 200 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6646 (pt) REVERT: C 23 LYS cc_start: 0.8004 (tttm) cc_final: 0.7709 (mtpt) REVERT: C 81 ILE cc_start: 0.8243 (mm) cc_final: 0.7944 (mm) REVERT: C 95 TRP cc_start: 0.7910 (p-90) cc_final: 0.7446 (p-90) outliers start: 19 outliers final: 15 residues processed: 109 average time/residue: 0.2263 time to fit residues: 31.7298 Evaluate side-chains 113 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 199 VAL 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 119 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7040 Z= 0.306 Angle : 0.649 8.626 9571 Z= 0.315 Chirality : 0.041 0.203 1140 Planarity : 0.005 0.067 1132 Dihedral : 11.182 72.324 1791 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.43 % Allowed : 14.12 % 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: -0.67 (0.28), residues: 865 helix: 1.38 (0.26), residues: 379 sheet: -1.23 (0.36), residues: 198 loop : -2.33 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.022 0.002 PHE B 89 TYR 0.014 0.002 TYR A 141 ARG 0.001 0.000 ARG C 13 *********************** 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 120 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.666 Fit side-chains REVERT: A 263 LYS cc_start: 0.8337 (mmpt) cc_final: 0.8051 (mmmt) REVERT: A 276 MET cc_start: 0.6354 (mmm) cc_final: 0.5908 (mmt) REVERT: A 411 LYS cc_start: 0.8702 (tmmt) cc_final: 0.8476 (tmtt) REVERT: B 91 LYS cc_start: 0.8451 (mttt) cc_final: 0.8116 (mtpt) REVERT: B 105 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6308 (tm-30) REVERT: B 200 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6797 (pt) REVERT: C 29 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: C 81 ILE cc_start: 0.8262 (mm) cc_final: 0.7926 (mm) REVERT: C 95 TRP cc_start: 0.7965 (p-90) cc_final: 0.7481 (p-90) outliers start: 27 outliers final: 20 residues processed: 112 average time/residue: 0.2019 time to fit residues: 29.7366 Evaluate side-chains 115 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 199 VAL 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 36 ASN Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 29 GLU 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 9 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 0.0470 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.3888 ------------------------------------------------------------------------------- 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 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7040 Z= 0.193 Angle : 0.595 6.486 9571 Z= 0.284 Chirality : 0.039 0.180 1140 Planarity : 0.005 0.065 1132 Dihedral : 10.510 59.168 1791 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.79 % Allowed : 15.76 % 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: -0.39 (0.29), residues: 865 helix: 1.64 (0.27), residues: 381 sheet: -1.12 (0.36), residues: 200 loop : -2.25 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 344 HIS 0.001 0.001 HIS A 156 PHE 0.016 0.001 PHE C 38 TYR 0.010 0.001 TYR A 251 ARG 0.001 0.000 ARG C 40 *********************** 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 112 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.790 Fit side-chains REVERT: A 263 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7979 (mmmt) REVERT: A 276 MET cc_start: 0.6353 (mmm) cc_final: 0.5908 (mmt) REVERT: A 303 LEU cc_start: 0.8781 (mt) cc_final: 0.8350 (mp) REVERT: A 411 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8539 (tmtt) REVERT: B 91 LYS cc_start: 0.8382 (mttt) cc_final: 0.8039 (mtpt) REVERT: B 105 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.6152 (tm-30) REVERT: B 200 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6826 (pt) REVERT: C 23 LYS cc_start: 0.7971 (tttm) cc_final: 0.7712 (mtpt) REVERT: C 81 ILE cc_start: 0.8158 (mm) cc_final: 0.7834 (mm) REVERT: C 95 TRP cc_start: 0.7909 (p-90) cc_final: 0.7420 (p-90) outliers start: 17 outliers final: 13 residues processed: 104 average time/residue: 0.1975 time to fit residues: 27.1694 Evaluate side-chains 107 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 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 153 ASN C 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7040 Z= 0.255 Angle : 0.623 7.797 9571 Z= 0.299 Chirality : 0.040 0.228 1140 Planarity : 0.005 0.066 1132 Dihedral : 10.384 59.077 1791 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.45 % Allowed : 15.11 % 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: -0.47 (0.29), residues: 865 helix: 1.56 (0.26), residues: 383 sheet: -1.22 (0.36), residues: 200 loop : -2.25 (0.34), residues: 282 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 0.002 PHE B 89 TYR 0.011 0.001 TYR A 141 ARG 0.001 0.000 ARG C 13 *********************** 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 118 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.709 Fit side-chains REVERT: A 263 LYS cc_start: 0.8258 (mmpt) cc_final: 0.7883 (mmmt) REVERT: A 276 MET cc_start: 0.6288 (mmm) cc_final: 0.5842 (mmt) REVERT: A 303 LEU cc_start: 0.8734 (mt) cc_final: 0.8282 (mp) REVERT: A 411 LYS cc_start: 0.8794 (tmmt) cc_final: 0.8573 (tmtt) REVERT: B 91 LYS cc_start: 0.8409 (mttt) cc_final: 0.8065 (mtpt) REVERT: B 105 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6130 (tm-30) REVERT: B 200 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6808 (pt) REVERT: C 23 LYS cc_start: 0.7971 (tttm) cc_final: 0.7703 (mtpt) REVERT: C 29 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: C 81 ILE cc_start: 0.8202 (mm) cc_final: 0.7868 (mm) REVERT: C 95 TRP cc_start: 0.7940 (p-90) cc_final: 0.7436 (p-90) outliers start: 21 outliers final: 17 residues processed: 108 average time/residue: 0.2354 time to fit residues: 32.5281 Evaluate side-chains 115 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 199 VAL 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 476 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 29 GLU 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 79 optimal weight: 0.1980 chunk 46 optimal weight: 0.0050 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.2752 ------------------------------------------------------------------------------- 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 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7040 Z= 0.170 Angle : 0.577 8.085 9571 Z= 0.277 Chirality : 0.039 0.164 1140 Planarity : 0.004 0.065 1132 Dihedral : 9.991 59.549 1791 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.28 % Allowed : 15.93 % Favored : 80.79 % 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: -0.31 (0.29), residues: 865 helix: 1.76 (0.26), residues: 381 sheet: -1.14 (0.36), residues: 201 loop : -2.25 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 344 HIS 0.001 0.001 HIS A 156 PHE 0.013 0.001 PHE C 38 TYR 0.010 0.001 TYR A 251 ARG 0.001 0.000 ARG C 40 *********************** 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 110 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.664 Fit side-chains REVERT: A 263 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7938 (mmmt) REVERT: A 276 MET cc_start: 0.6218 (mmm) cc_final: 0.5786 (mmt) REVERT: A 303 LEU cc_start: 0.8673 (mt) cc_final: 0.8244 (mp) REVERT: B 91 LYS cc_start: 0.8397 (mttt) cc_final: 0.8008 (mtpt) REVERT: B 105 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.6058 (tm-30) REVERT: B 200 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6900 (pt) REVERT: C 81 ILE cc_start: 0.8160 (mm) cc_final: 0.7857 (mm) REVERT: C 95 TRP cc_start: 0.7813 (p-90) cc_final: 0.7323 (p-90) outliers start: 20 outliers final: 17 residues processed: 102 average time/residue: 0.2034 time to fit residues: 27.4020 Evaluate side-chains 105 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 199 VAL 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 476 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.4980 chunk 56 optimal weight: 0.0030 chunk 85 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7040 Z= 0.242 Angle : 0.611 8.180 9571 Z= 0.294 Chirality : 0.040 0.208 1140 Planarity : 0.005 0.064 1132 Dihedral : 9.970 59.971 1791 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.28 % Allowed : 15.76 % Favored : 80.95 % 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: -0.39 (0.29), residues: 865 helix: 1.72 (0.26), residues: 380 sheet: -1.16 (0.36), residues: 199 loop : -2.34 (0.34), residues: 286 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 0.018 0.001 PHE B 89 TYR 0.012 0.001 TYR B 48 ARG 0.001 0.000 ARG C 31 ********************** 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 fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.635 Fit side-chains REVERT: A 170 GLN cc_start: 0.8280 (tp40) cc_final: 0.8073 (tp40) REVERT: A 263 LYS cc_start: 0.8234 (mmpt) cc_final: 0.7937 (mmmt) REVERT: A 276 MET cc_start: 0.6200 (mmm) cc_final: 0.5767 (mmt) REVERT: A 303 LEU cc_start: 0.8675 (mt) cc_final: 0.8226 (mp) REVERT: A 353 LYS cc_start: 0.7744 (ptpt) cc_final: 0.7522 (pttt) REVERT: B 91 LYS cc_start: 0.8448 (mttt) cc_final: 0.8066 (mtpt) REVERT: B 105 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6106 (tm-30) REVERT: B 200 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6855 (pt) REVERT: C 23 LYS cc_start: 0.7945 (tttm) cc_final: 0.7715 (mtpt) REVERT: C 81 ILE cc_start: 0.8221 (mm) cc_final: 0.7900 (mm) REVERT: C 95 TRP cc_start: 0.7935 (p-90) cc_final: 0.7438 (p-90) outliers start: 20 outliers final: 18 residues processed: 106 average time/residue: 0.2422 time to fit residues: 32.7361 Evaluate side-chains 113 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 199 VAL 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 476 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 0.0040 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 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** C 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.172378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134606 restraints weight = 18129.006| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 4.48 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7040 Z= 0.235 Angle : 0.607 8.196 9571 Z= 0.293 Chirality : 0.040 0.189 1140 Planarity : 0.005 0.064 1132 Dihedral : 9.853 59.989 1791 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.12 % Allowed : 16.26 % Favored : 80.62 % 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: -0.38 (0.29), residues: 865 helix: 1.72 (0.26), residues: 380 sheet: -1.15 (0.36), residues: 201 loop : -2.33 (0.34), residues: 284 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 0.017 0.001 PHE B 89 TYR 0.012 0.001 TYR B 48 ARG 0.001 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.72 seconds wall clock time: 33 minutes 56.08 seconds (2036.08 seconds total)