Starting phenix.real_space_refine on Tue Mar 3 18:38:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2t_27149/03_2026/8d2t_27149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2t_27149/03_2026/8d2t_27149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2t_27149/03_2026/8d2t_27149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2t_27149/03_2026/8d2t_27149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2t_27149/03_2026/8d2t_27149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2t_27149/03_2026/8d2t_27149.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.042 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 1606 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4322 2.51 5 N 1015 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6609 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3380 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 7, 'GLN:plan1': 7, 'ASN:plan1': 5, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 134 Conformer: "B" Number of residues, atoms: 460, 3380 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 7, 'GLN:plan1': 7, 'ASN:plan1': 5, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 134 bond proxies already assigned to first conformer: 3432 Chain: "B" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1395 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 6, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1412 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 9, 315 Unusual residues: {'LMT': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Conformer: "B" Number of residues, atoms: 9, 315 Unusual residues: {'LMT': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} bond proxies already assigned to first conformer: 288 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} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 323 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 323 " occ=0.50 residue: pdb=" N APHE A 396 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 396 " 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 603 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 603 " occ=0.50 Time building chain proxies: 2.16, per 1000 atoms: 0.33 Number of scatterers: 6609 At special positions: 0 Unit cell: (69.208, 72.584, 141.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1239 8.00 N 1015 7.00 C 4322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 458.8 milliseconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 45.1% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.630A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 68 removed outlier: 4.034A pdb=" N GLN A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.646A pdb=" N ILE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (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: 3.521A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.593A pdb=" N TRP A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.456A pdb=" N SER A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 197 removed outlier: 3.520A pdb=" N THR A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 261 removed outlier: 3.694A pdb=" N ALA A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 288 through 311 removed outlier: 4.062A pdb=" N GLY A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 325 through 351 removed outlier: 3.769A pdb=" N LEU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.694A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.046A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 414 removed outlier: 3.796A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 421 through 451 Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.658A pdb=" N SER A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 495 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'C' and resid 28 through 31 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.446A pdb=" N VAL B 32 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR B 48 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.993A pdb=" N ALA B 127 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE B 174 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL B 129 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU B 172 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N PHE B 131 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA B 170 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N MET B 168 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.842A 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 removed outlier: 3.531A pdb=" N ALA C 18 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 76 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 58 removed outlier: 5.158A pdb=" N TRP C 46 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE C 38 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 121 through 123 removed outlier: 6.042A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123 removed outlier: 6.042A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 149 through 151 376 hydrogen bonds defined for protein. 1064 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: 1.07 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1947 1.34 - 1.46: 1719 1.46 - 1.58: 3055 1.58 - 1.70: 22 1.70 - 1.81: 46 Bond restraints: 6789 Sorted by residual: bond pdb=" C1B LMT A 601 " pdb=" O5B LMT A 601 " ideal model delta sigma weight residual 1.393 1.515 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C1B LMT A 602 " pdb=" O5B LMT A 602 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1BALMT A 603 " pdb=" O5BALMT A 603 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C1BBLMT A 603 " pdb=" O5BBLMT A 603 " ideal model delta sigma weight residual 1.393 1.512 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 6784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8772 1.91 - 3.81: 311 3.81 - 5.72: 99 5.72 - 7.62: 78 7.62 - 9.53: 14 Bond angle restraints: 9274 Sorted by residual: angle pdb=" C THR A 90 " pdb=" N ASP A 91 " pdb=" CA ASP A 91 " ideal model delta sigma weight residual 121.80 112.97 8.83 2.44e+00 1.68e-01 1.31e+01 angle pdb=" N GLY B 97 " pdb=" CA GLY B 97 " pdb=" C GLY B 97 " ideal model delta sigma weight residual 113.18 121.74 -8.56 2.37e+00 1.78e-01 1.30e+01 angle pdb=" N TRP C 95 " pdb=" CA TRP C 95 " pdb=" C TRP C 95 " ideal model delta sigma weight residual 109.24 103.88 5.36 1.67e+00 3.59e-01 1.03e+01 angle pdb=" C1B LMT A 606 " pdb=" O1B LMT A 606 " pdb=" C4' LMT A 606 " ideal model delta sigma weight residual 117.87 108.34 9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N ASP A 235 " pdb=" CA ASP A 235 " pdb=" C ASP A 235 " ideal model delta sigma weight residual 112.89 108.96 3.93 1.24e+00 6.50e-01 1.00e+01 ... (remaining 9269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.38: 3866 23.38 - 46.76: 229 46.76 - 70.14: 86 70.14 - 93.52: 52 93.52 - 116.90: 96 Dihedral angle restraints: 4329 sinusoidal: 1865 harmonic: 2464 Sorted by residual: dihedral pdb=" CA ARG A 455 " pdb=" C ARG A 455 " pdb=" N GLY A 456 " pdb=" CA GLY A 456 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C1B LMT A 602 " pdb=" C2B LMT A 602 " pdb=" C3B LMT A 602 " pdb=" O3B LMT A 602 " ideal model delta sinusoidal sigma weight residual -175.52 -58.62 -116.90 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" O2B LMT A 606 " pdb=" C2B LMT A 606 " pdb=" C3B LMT A 606 " pdb=" O3B LMT A 606 " ideal model delta sinusoidal sigma weight residual 63.73 -179.47 -116.80 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 4326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 825 0.050 - 0.100: 219 0.100 - 0.150: 56 0.150 - 0.200: 10 0.200 - 0.250: 2 Chirality restraints: 1112 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 -2.45 0.25 2.00e-01 2.50e+01 1.56e+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 -2.35 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1B LMT A 608 " pdb=" C2B LMT A 608 " pdb=" O1B LMT A 608 " pdb=" O5B LMT A 608 " both_signs ideal model delta sigma weight residual False -2.20 -2.40 0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 1109 not shown) Planarity restraints: 1119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 251 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C TYR A 251 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR A 251 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 252 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 103 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO C 104 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO C 47 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " 0.030 5.00e-02 4.00e+02 ... (remaining 1116 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1503 2.79 - 3.31: 6082 3.31 - 3.84: 11173 3.84 - 4.37: 12312 4.37 - 4.90: 22184 Nonbonded interactions: 53254 Sorted by model distance: nonbonded pdb=" O TRP A 86 " pdb=" OG1 THR A 90 " model vdw 2.257 3.040 nonbonded pdb=" O TYR A 452 " pdb=" ND2 ASN C 99 " model vdw 2.275 3.120 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.281 3.040 nonbonded pdb=" O GLN A 135 " pdb=" O6' LMT A 608 " model vdw 2.301 3.040 nonbonded pdb=" NZ LYS B 11 " pdb=" O ARG B 19 " model vdw 2.304 3.120 ... (remaining 53249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.011 0.122 6794 Z= 0.533 Angle : 1.101 9.528 9284 Z= 0.457 Chirality : 0.050 0.250 1112 Planarity : 0.006 0.055 1119 Dihedral : 27.925 116.897 2744 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.51 % Allowed : 8.22 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.28), residues: 865 helix: 0.61 (0.26), residues: 376 sheet: -0.59 (0.40), residues: 180 loop : -2.26 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.008 0.001 TYR A 251 PHE 0.029 0.002 PHE C 38 TRP 0.015 0.002 TRP C 33 HIS 0.004 0.002 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.01088 ( 6789) covalent geometry : angle 1.10146 ( 9274) SS BOND : bond 0.00260 ( 5) SS BOND : angle 0.68431 ( 10) hydrogen bonds : bond 0.13181 ( 363) hydrogen bonds : angle 6.80837 ( 1064) *********************** 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 152 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7700 (m-80) cc_final: 0.7475 (m-10) REVERT: A 109 MET cc_start: 0.8205 (mmt) cc_final: 0.7884 (mmt) REVERT: A 181 MET cc_start: 0.7940 (mtt) cc_final: 0.7675 (mtp) REVERT: A 189 LEU cc_start: 0.8416 (tp) cc_final: 0.8213 (tt) REVERT: A 427 PHE cc_start: 0.8184 (t80) cc_final: 0.7954 (t80) REVERT: B 60 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.6815 (mt0) outliers start: 3 outliers final: 0 residues processed: 151 average time/residue: 0.0897 time to fit residues: 17.7237 Evaluate side-chains 123 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 50.0000 chunk 74 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 195 GLN B 36 ASN C 50 ASN C 57 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141603 restraints weight = 22780.713| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.43 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6794 Z= 0.188 Angle : 0.869 11.580 9284 Z= 0.381 Chirality : 0.052 0.311 1112 Planarity : 0.005 0.053 1119 Dihedral : 19.796 80.473 1587 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.40 % Allowed : 11.64 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.29), residues: 865 helix: 1.36 (0.27), residues: 376 sheet: -0.49 (0.39), residues: 181 loop : -2.28 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 84 TYR 0.012 0.001 TYR A 159 PHE 0.024 0.002 PHE C 38 TRP 0.031 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 6789) covalent geometry : angle 0.86898 ( 9274) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.54149 ( 10) hydrogen bonds : bond 0.04121 ( 363) hydrogen bonds : angle 5.02098 ( 1064) *********************** 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 139 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7895 (mtt) cc_final: 0.7588 (mtp) REVERT: A 189 LEU cc_start: 0.8398 (tp) cc_final: 0.8186 (tt) REVERT: A 206 CYS cc_start: 0.5325 (m) cc_final: 0.4859 (m) REVERT: A 291 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.5739 (t80) REVERT: A 293 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7714 (mmtp) REVERT: B 60 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.6743 (mt0) REVERT: B 198 MET cc_start: 0.7731 (mmm) cc_final: 0.7148 (mmt) outliers start: 14 outliers final: 6 residues processed: 135 average time/residue: 0.0869 time to fit residues: 15.5279 Evaluate side-chains 121 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 44 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.0010 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 238 ASN C 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.163964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143827 restraints weight = 24588.550| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.03 r_work: 0.3173 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6794 Z= 0.173 Angle : 0.779 11.058 9284 Z= 0.354 Chirality : 0.048 0.338 1112 Planarity : 0.005 0.053 1119 Dihedral : 14.414 64.615 1587 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.54 % Allowed : 14.73 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.29), residues: 865 helix: 1.55 (0.27), residues: 375 sheet: -0.54 (0.39), residues: 181 loop : -2.28 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.009 0.001 TYR A 251 PHE 0.024 0.002 PHE C 38 TRP 0.026 0.002 TRP A 103 HIS 0.003 0.002 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6789) covalent geometry : angle 0.77850 ( 9274) SS BOND : bond 0.00197 ( 5) SS BOND : angle 1.38227 ( 10) hydrogen bonds : bond 0.03888 ( 363) hydrogen bonds : angle 4.71612 ( 1064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7984 (mtt) cc_final: 0.7712 (mtp) REVERT: A 189 LEU cc_start: 0.8533 (tp) cc_final: 0.8326 (tt) REVERT: A 291 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.5507 (t80) REVERT: A 293 LYS cc_start: 0.8024 (mmtp) cc_final: 0.7739 (mmtp) REVERT: B 60 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7132 (mt0) outliers start: 9 outliers final: 4 residues processed: 120 average time/residue: 0.0832 time to fit residues: 13.3093 Evaluate side-chains 119 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 163 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 0.0010 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.0570 chunk 76 optimal weight: 0.0770 overall best weight: 0.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.166617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143322 restraints weight = 36558.862| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 4.16 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6794 Z= 0.131 Angle : 0.718 10.780 9284 Z= 0.328 Chirality : 0.045 0.313 1112 Planarity : 0.005 0.052 1119 Dihedral : 12.973 59.794 1587 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.40 % Allowed : 14.38 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.29), residues: 865 helix: 1.80 (0.27), residues: 376 sheet: -0.48 (0.38), residues: 183 loop : -2.26 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.008 0.001 TYR A 251 PHE 0.020 0.002 PHE C 38 TRP 0.046 0.002 TRP A 103 HIS 0.001 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6789) covalent geometry : angle 0.71710 ( 9274) SS BOND : bond 0.00225 ( 5) SS BOND : angle 1.03601 ( 10) hydrogen bonds : bond 0.03548 ( 363) hydrogen bonds : angle 4.46234 ( 1064) *********************** 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 137 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.228 Fit side-chains REVERT: A 164 MET cc_start: 0.7560 (mmm) cc_final: 0.7183 (mmm) REVERT: A 173 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7454 (mtt90) REVERT: A 181 MET cc_start: 0.7885 (mtt) cc_final: 0.7565 (mtp) REVERT: A 291 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.5397 (t80) REVERT: A 318 TYR cc_start: 0.8572 (m-80) cc_final: 0.8194 (m-80) REVERT: B 60 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.6941 (mt0) REVERT: B 198 MET cc_start: 0.7728 (mmm) cc_final: 0.7316 (mmt) outliers start: 14 outliers final: 10 residues processed: 129 average time/residue: 0.0808 time to fit residues: 13.9012 Evaluate side-chains 127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.0030 chunk 44 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN C 50 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.164323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141399 restraints weight = 29341.342| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.76 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6794 Z= 0.182 Angle : 0.742 10.130 9284 Z= 0.347 Chirality : 0.046 0.269 1112 Planarity : 0.005 0.053 1119 Dihedral : 12.016 59.961 1587 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.25 % Allowed : 14.38 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 865 helix: 1.77 (0.27), residues: 376 sheet: -0.65 (0.38), residues: 187 loop : -2.33 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 61 TYR 0.010 0.001 TYR A 251 PHE 0.026 0.002 PHE C 38 TRP 0.045 0.002 TRP A 103 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6789) covalent geometry : angle 0.74082 ( 9274) SS BOND : bond 0.00169 ( 5) SS BOND : angle 1.45333 ( 10) hydrogen bonds : bond 0.03656 ( 363) hydrogen bonds : angle 4.51903 ( 1064) *********************** 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 140 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.230 Fit side-chains REVERT: A 164 MET cc_start: 0.7586 (mmm) cc_final: 0.7221 (mmm) REVERT: A 173 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7485 (mtt90) REVERT: A 181 MET cc_start: 0.7914 (mtt) cc_final: 0.7563 (mtp) REVERT: A 291 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.5657 (t80) REVERT: B 27 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 60 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7144 (mt0) REVERT: B 198 MET cc_start: 0.7728 (mmm) cc_final: 0.7436 (mmt) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.0878 time to fit residues: 15.2002 Evaluate side-chains 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 176 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 83 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: C 50 ASN C 112 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139674 restraints weight = 37330.406| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 4.46 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6794 Z= 0.190 Angle : 0.733 10.642 9284 Z= 0.346 Chirality : 0.045 0.248 1112 Planarity : 0.005 0.055 1119 Dihedral : 11.390 59.986 1587 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.60 % Allowed : 14.21 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.29), residues: 865 helix: 1.74 (0.27), residues: 377 sheet: -0.69 (0.39), residues: 180 loop : -2.28 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 191 TYR 0.009 0.001 TYR A 251 PHE 0.027 0.002 PHE C 38 TRP 0.030 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 6789) covalent geometry : angle 0.73227 ( 9274) SS BOND : bond 0.00166 ( 5) SS BOND : angle 1.31817 ( 10) hydrogen bonds : bond 0.03670 ( 363) hydrogen bonds : angle 4.54732 ( 1064) *********************** 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 143 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.218 Fit side-chains REVERT: A 164 MET cc_start: 0.7733 (mmm) cc_final: 0.7473 (mmm) REVERT: A 173 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7566 (mtt90) REVERT: A 181 MET cc_start: 0.7909 (mtt) cc_final: 0.7640 (mtp) REVERT: A 291 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.5175 (t80) REVERT: B 27 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 60 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: B 198 MET cc_start: 0.7966 (mmm) cc_final: 0.7682 (mmt) outliers start: 21 outliers final: 15 residues processed: 129 average time/residue: 0.0852 time to fit residues: 14.6367 Evaluate side-chains 136 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 0.0370 chunk 79 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 33 optimal weight: 0.0060 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144733 restraints weight = 28153.725| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.59 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6794 Z= 0.132 Angle : 0.677 10.067 9284 Z= 0.320 Chirality : 0.042 0.188 1112 Planarity : 0.005 0.054 1119 Dihedral : 10.466 59.284 1587 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.91 % Allowed : 15.41 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.30), residues: 865 helix: 1.96 (0.27), residues: 376 sheet: -0.48 (0.39), residues: 182 loop : -2.25 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 191 TYR 0.008 0.001 TYR A 251 PHE 0.023 0.002 PHE A 343 TRP 0.025 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6789) covalent geometry : angle 0.67575 ( 9274) SS BOND : bond 0.00209 ( 5) SS BOND : angle 1.27803 ( 10) hydrogen bonds : bond 0.03407 ( 363) hydrogen bonds : angle 4.35181 ( 1064) *********************** 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 137 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.217 Fit side-chains REVERT: A 164 MET cc_start: 0.7527 (mmm) cc_final: 0.7208 (mmm) REVERT: A 173 ARG cc_start: 0.7799 (mtt-85) cc_final: 0.7441 (mtt90) REVERT: A 181 MET cc_start: 0.7889 (mtt) cc_final: 0.7563 (mtp) REVERT: A 318 TYR cc_start: 0.8611 (m-80) cc_final: 0.8198 (m-80) REVERT: B 60 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7202 (mt0) REVERT: B 198 MET cc_start: 0.7683 (mmm) cc_final: 0.7463 (mmt) outliers start: 17 outliers final: 14 residues processed: 124 average time/residue: 0.0872 time to fit residues: 14.4160 Evaluate side-chains 127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 190 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.165176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141670 restraints weight = 32902.605| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 4.17 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6794 Z= 0.159 Angle : 0.699 9.805 9284 Z= 0.334 Chirality : 0.043 0.180 1112 Planarity : 0.005 0.053 1119 Dihedral : 10.376 59.683 1587 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.25 % Allowed : 16.27 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.30), residues: 865 helix: 1.88 (0.27), residues: 377 sheet: -0.52 (0.40), residues: 176 loop : -2.22 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.009 0.001 TYR A 251 PHE 0.024 0.002 PHE C 38 TRP 0.025 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6789) covalent geometry : angle 0.69867 ( 9274) SS BOND : bond 0.00204 ( 5) SS BOND : angle 1.12592 ( 10) hydrogen bonds : bond 0.03537 ( 363) hydrogen bonds : angle 4.38558 ( 1064) *********************** 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 135 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.214 Fit side-chains REVERT: A 164 MET cc_start: 0.7620 (mmm) cc_final: 0.7385 (mmm) REVERT: A 173 ARG cc_start: 0.7846 (mtt-85) cc_final: 0.7488 (mtt90) REVERT: A 181 MET cc_start: 0.7953 (mtt) cc_final: 0.7613 (mtp) REVERT: A 291 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.5711 (t80) REVERT: B 60 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7619 (mt0) outliers start: 19 outliers final: 12 residues processed: 120 average time/residue: 0.0895 time to fit residues: 14.3109 Evaluate side-chains 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN C 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.163731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140154 restraints weight = 37061.420| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 4.33 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 0.052 6794 Z= 0.184 Angle : 0.707 10.195 9284 Z= 0.341 Chirality : 0.043 0.192 1112 Planarity : 0.005 0.053 1119 Dihedral : 10.207 59.765 1587 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.42 % Allowed : 16.10 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.30), residues: 865 helix: 1.86 (0.27), residues: 376 sheet: -0.60 (0.41), residues: 163 loop : -2.31 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 191 TYR 0.010 0.001 TYR A 251 PHE 0.026 0.002 PHE C 38 TRP 0.023 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 6789) covalent geometry : angle 0.70629 ( 9274) SS BOND : bond 0.00171 ( 5) SS BOND : angle 1.18086 ( 10) hydrogen bonds : bond 0.03595 ( 363) hydrogen bonds : angle 4.47153 ( 1064) *********************** 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 133 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.222 Fit side-chains REVERT: A 173 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7499 (mtt90) REVERT: A 181 MET cc_start: 0.8024 (mtt) cc_final: 0.7785 (mtp) REVERT: A 291 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6212 (t80) REVERT: B 60 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7878 (mt0) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.0872 time to fit residues: 13.8559 Evaluate side-chains 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 76 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 53 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 49 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 ASN C 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142881 restraints weight = 36339.427| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 4.12 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6794 Z= 0.139 Angle : 0.696 13.452 9284 Z= 0.327 Chirality : 0.042 0.182 1112 Planarity : 0.005 0.054 1119 Dihedral : 9.877 59.917 1587 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.57 % Allowed : 17.64 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.30), residues: 865 helix: 1.94 (0.27), residues: 376 sheet: -0.47 (0.39), residues: 185 loop : -2.23 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.008 0.001 TYR A 251 PHE 0.023 0.001 PHE C 38 TRP 0.022 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6789) covalent geometry : angle 0.69541 ( 9274) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.09613 ( 10) hydrogen bonds : bond 0.03434 ( 363) hydrogen bonds : angle 4.37241 ( 1064) ********************** 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 133 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.248 Fit side-chains REVERT: A 181 MET cc_start: 0.7946 (mtt) cc_final: 0.7618 (mtp) REVERT: A 291 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6078 (t80) REVERT: A 318 TYR cc_start: 0.8537 (m-80) cc_final: 0.8141 (m-80) REVERT: A 424 PHE cc_start: 0.7968 (t80) cc_final: 0.7564 (t80) REVERT: B 60 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: B 198 MET cc_start: 0.7350 (mmm) cc_final: 0.6825 (mmt) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 0.0886 time to fit residues: 14.3881 Evaluate side-chains 127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 431 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.164418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.141767 restraints weight = 28971.968| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.65 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6794 Z= 0.165 Angle : 0.718 12.304 9284 Z= 0.338 Chirality : 0.042 0.185 1112 Planarity : 0.005 0.053 1119 Dihedral : 9.838 59.798 1587 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.74 % Allowed : 18.32 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.30), residues: 865 helix: 1.89 (0.27), residues: 376 sheet: -0.46 (0.39), residues: 182 loop : -2.27 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.009 0.001 TYR A 251 PHE 0.024 0.002 PHE C 38 TRP 0.021 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6789) covalent geometry : angle 0.71787 ( 9274) SS BOND : bond 0.00184 ( 5) SS BOND : angle 1.12951 ( 10) hydrogen bonds : bond 0.03509 ( 363) hydrogen bonds : angle 4.36231 ( 1064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.72 seconds wall clock time: 26 minutes 6.05 seconds (1566.05 seconds total)