Starting phenix.real_space_refine on Thu Jul 2 09:12:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2t_27149/07_2026/8d2t_27149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2t_27149/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8d2t_27149/07_2026/8d2t_27149.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2t_27149/07_2026/8d2t_27149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2t_27149/07_2026/8d2t_27149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2t_27149/07_2026/8d2t_27149.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2t_27149/07_2026/8d2t_27149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2t_27149/07_2026/8d2t_27149.cif" } 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-6108/lib/python3.11/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: 1.63, per 1000 atoms: 0.25 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: 0.49 Conformation dependent library (CDL) restraints added in 497.5 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: 0.17 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: 0.77 Time building geometry restraints manager: 0.69 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 - 17.31: 3495 17.31 - 34.61: 208 34.61 - 51.92: 63 51.92 - 69.22: 12 69.22 - 86.53: 1 Dihedral angle restraints: 3779 sinusoidal: 1315 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=" CA GLY A 136 " pdb=" C GLY A 136 " pdb=" N LYS A 137 " pdb=" CA LYS A 137 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY C 54 " pdb=" C GLY C 54 " pdb=" N PRO C 55 " pdb=" CA PRO C 55 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3776 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: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.950 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 12.859 86.529 2194 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/Z covalent geometry : bond 0.01088 / 0.53 ( 6789) covalent geometry : angle 1.10146 / 0.46 ( 9274) SS BOND : bond 0.00260 / 0.13 ( 5) SS BOND : angle 0.68431 / 0.45 ( 10) hydrogen bonds : bond 0.13181 / 9.44 ( 363) hydrogen bonds : angle 6.80837 / 4.87 ( 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 : 0.146 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: 0.0670 time to fit residues: 13.3170 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 : 0.131 ------------------------------------------------------------------------------- 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... A 149 GLN A 195 GLN A 197 GLN B 36 ASN B 37 GLN C 50 ASN C 57 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146833 restraints weight = 22479.596| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.54 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6794 Z= 0.173 Angle : 0.698 11.060 9284 Z= 0.338 Chirality : 0.043 0.239 1112 Planarity : 0.005 0.053 1119 Dihedral : 11.121 59.285 1037 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.57 % Allowed : 11.13 % Favored : 86.30 % 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: 1.35 (0.27), residues: 376 sheet: -0.50 (0.39), residues: 181 loop : -2.26 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 84 TYR 0.010 0.001 TYR A 159 PHE 0.023 0.002 PHE C 38 TRP 0.027 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 6789) covalent geometry : angle 0.69807 / 0.34 ( 9274) SS BOND : bond 0.00394 / 0.21 ( 5) SS BOND : angle 0.81519 / 0.45 ( 10) hydrogen bonds : bond 0.04250 / 2.93 ( 363) hydrogen bonds : angle 5.09188 / 3.69 ( 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 140 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.8064 (mtt) cc_final: 0.7801 (mtp) REVERT: A 206 CYS cc_start: 0.5245 (m) cc_final: 0.4814 (m) REVERT: A 291 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.5878 (t80) REVERT: B 60 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7010 (mt0) REVERT: B 198 MET cc_start: 0.7014 (mmm) cc_final: 0.6580 (mmt) REVERT: C 25 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7276 (mmtt) outliers start: 15 outliers final: 6 residues processed: 134 average time/residue: 0.0698 time to fit residues: 12.4626 Evaluate side-chains 120 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 163 SER 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: 0.3980 chunk 71 optimal weight: 0.0000 chunk 4 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 81 optimal weight: 0.0870 overall best weight: 0.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.167044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145685 restraints weight = 24376.687| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.33 r_work: 0.3216 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2075 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= 0.125 Angle : 0.659 10.914 9284 Z= 0.313 Chirality : 0.042 0.215 1112 Planarity : 0.005 0.050 1119 Dihedral : 10.333 58.871 1037 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.71 % Allowed : 13.53 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.29), residues: 865 helix: 1.69 (0.27), residues: 374 sheet: -0.48 (0.38), residues: 183 loop : -2.17 (0.34), residues: 308 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 0.021 0.002 PHE A 427 TRP 0.027 0.002 TRP A 344 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 6789) covalent geometry : angle 0.65747 / 0.31 ( 9274) SS BOND : bond 0.00294 / 0.16 ( 5) SS BOND : angle 1.48976 / 0.89 ( 10) hydrogen bonds : bond 0.03728 / 2.54 ( 363) hydrogen bonds : angle 4.61903 / 3.35 ( 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 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7853 (mtt) cc_final: 0.7544 (mtp) REVERT: A 291 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.5183 (t80) REVERT: A 318 TYR cc_start: 0.8859 (m-80) cc_final: 0.8380 (m-80) REVERT: B 60 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.6914 (mt0) outliers start: 10 outliers final: 5 residues processed: 126 average time/residue: 0.0706 time to fit residues: 11.8328 Evaluate side-chains 122 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 76 optimal weight: 0.0970 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 ASN 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 = 0.3964 r_free = 0.3964 target = 0.165770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144430 restraints weight = 36302.574| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.81 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6794 Z= 0.138 Angle : 0.660 10.611 9284 Z= 0.314 Chirality : 0.042 0.185 1112 Planarity : 0.005 0.048 1119 Dihedral : 10.066 58.746 1037 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.74 % Allowed : 12.33 % Favored : 84.93 % 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: 1.83 (0.27), residues: 376 sheet: -0.44 (0.38), residues: 183 loop : -2.14 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 191 TYR 0.009 0.001 TYR A 251 PHE 0.021 0.002 PHE C 38 TRP 0.027 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6789) covalent geometry : angle 0.65964 / 0.31 ( 9274) SS BOND : bond 0.00208 / 0.11 ( 5) SS BOND : angle 1.07550 / 0.62 ( 10) hydrogen bonds : bond 0.03578 / 2.43 ( 363) hydrogen bonds : angle 4.44606 / 3.22 ( 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 135 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.154 Fit side-chains REVERT: A 164 MET cc_start: 0.7473 (mmm) cc_final: 0.7060 (mmm) REVERT: A 173 ARG cc_start: 0.7784 (mtt-85) cc_final: 0.7523 (mtt90) REVERT: A 181 MET cc_start: 0.7930 (mtt) cc_final: 0.7629 (mtp) REVERT: A 291 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.5434 (t80) REVERT: B 60 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.6820 (mt0) REVERT: B 198 MET cc_start: 0.7752 (mmm) cc_final: 0.7359 (mmt) outliers start: 16 outliers final: 12 residues processed: 127 average time/residue: 0.0688 time to fit residues: 11.5670 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 : 0.157 ------------------------------------------------------------------------------- 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 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 439 SER 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 163 SER Chi-restraints excluded: chain C residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 50 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 = 0.3920 r_free = 0.3920 target = 0.161578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138537 restraints weight = 28809.605| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.86 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6794 Z= 0.234 Angle : 0.738 10.901 9284 Z= 0.356 Chirality : 0.044 0.155 1112 Planarity : 0.005 0.052 1119 Dihedral : 10.293 59.504 1037 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.25 % Allowed : 13.70 % Favored : 83.05 % 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: -0.25 (0.29), residues: 865 helix: 1.65 (0.27), residues: 376 sheet: -0.65 (0.38), residues: 187 loop : -2.23 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.010 0.001 TYR A 251 PHE 0.029 0.002 PHE C 38 TRP 0.029 0.003 TRP A 344 HIS 0.004 0.002 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 ( 6789) covalent geometry : angle 0.73690 / 0.36 ( 9274) SS BOND : bond 0.00131 / 0.07 ( 5) SS BOND : angle 1.64743 / 0.93 ( 10) hydrogen bonds : bond 0.03834 / 2.61 ( 363) hydrogen bonds : angle 4.63592 / 3.37 ( 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 136 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.231 Fit side-chains REVERT: A 164 MET cc_start: 0.7637 (mmm) cc_final: 0.7238 (mmm) REVERT: A 173 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7507 (mtt90) REVERT: A 181 MET cc_start: 0.7978 (mtt) cc_final: 0.7695 (mtp) REVERT: A 291 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.5993 (t80) REVERT: B 60 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.6979 (mt0) REVERT: B 198 MET cc_start: 0.7849 (mmm) cc_final: 0.7547 (mmt) outliers start: 19 outliers final: 14 residues processed: 125 average time/residue: 0.0709 time to fit residues: 11.8473 Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 291 TYR Chi-restraints excluded: chain A residue 303 LEU 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 63 GLN Chi-restraints excluded: chain B residue 168 MET 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 163 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3933 r_free = 0.3933 target = 0.162940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139249 restraints weight = 36179.213| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.45 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2344 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= 0.172 Angle : 0.691 10.823 9284 Z= 0.332 Chirality : 0.043 0.152 1112 Planarity : 0.005 0.053 1119 Dihedral : 9.837 57.995 1037 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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: -0.19 (0.29), residues: 865 helix: 1.74 (0.27), residues: 376 sheet: -0.61 (0.38), residues: 187 loop : -2.27 (0.34), residues: 302 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 0.026 0.002 PHE C 38 TRP 0.029 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 6789) covalent geometry : angle 0.69019 / 0.33 ( 9274) SS BOND : bond 0.00160 / 0.09 ( 5) SS BOND : angle 1.44634 / 0.84 ( 10) hydrogen bonds : bond 0.03642 / 2.48 ( 363) hydrogen bonds : angle 4.52804 / 3.29 ( 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 137 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.173 Fit side-chains REVERT: A 164 MET cc_start: 0.7745 (mmm) cc_final: 0.7347 (mmm) REVERT: A 173 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7503 (mtt90) REVERT: A 181 MET cc_start: 0.7880 (mtt) cc_final: 0.7604 (mtp) REVERT: A 291 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.5183 (t80) REVERT: B 60 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.6981 (mt0) REVERT: B 198 MET cc_start: 0.8102 (mmm) cc_final: 0.7818 (mmt) outliers start: 21 outliers final: 14 residues processed: 124 average time/residue: 0.0684 time to fit residues: 11.3703 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 : 0.202 ------------------------------------------------------------------------------- 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 291 TYR Chi-restraints excluded: chain A residue 431 PHE 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 139 ILE Chi-restraints excluded: chain B residue 168 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 0.0970 chunk 79 optimal weight: 9.9990 chunk 80 optimal weight: 0.4980 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3964 r_free = 0.3964 target = 0.165838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144444 restraints weight = 27097.923| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.53 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2528 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= 0.127 Angle : 0.650 9.901 9284 Z= 0.310 Chirality : 0.041 0.146 1112 Planarity : 0.005 0.053 1119 Dihedral : 9.204 58.384 1037 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.08 % Allowed : 15.07 % Favored : 81.85 % 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: 1.98 (0.27), residues: 376 sheet: -0.45 (0.38), residues: 189 loop : -2.28 (0.34), residues: 300 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 0.021 0.001 PHE C 38 TRP 0.029 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6789) covalent geometry : angle 0.64901 / 0.31 ( 9274) SS BOND : bond 0.00256 / 0.14 ( 5) SS BOND : angle 1.33105 / 0.79 ( 10) hydrogen bonds : bond 0.03385 / 2.29 ( 363) hydrogen bonds : angle 4.31218 / 3.13 ( 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 138 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.151 Fit side-chains REVERT: A 164 MET cc_start: 0.7444 (mmm) cc_final: 0.7159 (mmm) REVERT: A 173 ARG cc_start: 0.7714 (mtt-85) cc_final: 0.7428 (mtt90) REVERT: A 181 MET cc_start: 0.7939 (mtt) cc_final: 0.7649 (mtp) REVERT: A 318 TYR cc_start: 0.8613 (m-80) cc_final: 0.8201 (m-80) REVERT: B 60 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: B 198 MET cc_start: 0.7602 (mmm) cc_final: 0.7395 (mmt) outliers start: 18 outliers final: 14 residues processed: 125 average time/residue: 0.0640 time to fit residues: 10.8010 Evaluate side-chains 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 431 PHE 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 139 ILE Chi-restraints excluded: chain B residue 168 MET 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: 5.9990 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.0570 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN C 112 ASN C 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.164920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142605 restraints weight = 32105.064| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 4.00 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6794 Z= 0.138 Angle : 0.664 9.238 9284 Z= 0.317 Chirality : 0.042 0.148 1112 Planarity : 0.005 0.051 1119 Dihedral : 8.961 58.917 1037 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.08 % Allowed : 15.92 % Favored : 80.99 % 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: 1.95 (0.27), residues: 377 sheet: -0.44 (0.39), residues: 182 loop : -2.22 (0.33), 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 0.023 0.002 PHE C 38 TRP 0.026 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6789) covalent geometry : angle 0.66348 / 0.32 ( 9274) SS BOND : bond 0.00377 / 0.20 ( 5) SS BOND : angle 1.08267 / 0.64 ( 10) hydrogen bonds : bond 0.03399 / 2.30 ( 363) hydrogen bonds : angle 4.25186 / 3.08 ( 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 137 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.208 Fit side-chains REVERT: A 173 ARG cc_start: 0.7829 (mtt-85) cc_final: 0.7491 (mtt90) REVERT: A 181 MET cc_start: 0.7945 (mtt) cc_final: 0.7607 (mtp) REVERT: A 291 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.5185 (t80) REVERT: A 318 TYR cc_start: 0.8636 (m-80) cc_final: 0.8257 (m-80) REVERT: B 60 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7226 (mt0) REVERT: B 198 MET cc_start: 0.7922 (mmm) cc_final: 0.7718 (mmt) outliers start: 18 outliers final: 12 residues processed: 123 average time/residue: 0.0664 time to fit residues: 10.7566 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 : 0.138 ------------------------------------------------------------------------------- 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 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 139 ILE Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 168 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.0070 chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN C 112 ASN C 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143005 restraints weight = 36131.990| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.89 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6794 Z= 0.145 Angle : 0.675 11.289 9284 Z= 0.322 Chirality : 0.042 0.149 1112 Planarity : 0.005 0.051 1119 Dihedral : 8.861 56.502 1037 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.08 % Allowed : 16.95 % Favored : 79.97 % 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: 1.92 (0.27), residues: 376 sheet: -0.40 (0.39), residues: 182 loop : -2.23 (0.33), residues: 307 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 0.024 0.002 PHE A 427 TRP 0.023 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6789) covalent geometry : angle 0.67495 / 0.32 ( 9274) SS BOND : bond 0.00198 / 0.11 ( 5) SS BOND : angle 1.05980 / 0.62 ( 10) hydrogen bonds : bond 0.03385 / 2.30 ( 363) hydrogen bonds : angle 4.33068 / 3.16 ( 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 132 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.146 Fit side-chains REVERT: A 181 MET cc_start: 0.7901 (mtt) cc_final: 0.7574 (mtp) REVERT: A 291 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.5248 (t80) REVERT: A 318 TYR cc_start: 0.8582 (m-80) cc_final: 0.8212 (m-80) REVERT: B 60 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: B 153 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7079 (p0) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 0.0664 time to fit residues: 10.3932 Evaluate side-chains 126 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 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 139 ILE Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 168 MET 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: 0.1980 chunk 83 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3945 r_free = 0.3945 target = 0.164265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141262 restraints weight = 35605.296| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.28 r_work (final): 0.3677 ------------------------------------------------------------------------------- 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 = 0.23 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 = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6794 Z= 0.155 Angle : 0.689 13.502 9284 Z= 0.328 Chirality : 0.043 0.159 1112 Planarity : 0.005 0.051 1119 Dihedral : 8.849 55.289 1037 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.08 % Allowed : 17.47 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.29), residues: 865 helix: 1.83 (0.27), residues: 377 sheet: -0.39 (0.39), residues: 182 loop : -2.29 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 191 TYR 0.012 0.001 TYR A 358 PHE 0.024 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/Z covalent geometry : bond 0.00366 / 0.16 ( 6789) covalent geometry : angle 0.68843 / 0.33 ( 9274) SS BOND : bond 0.00192 / 0.10 ( 5) SS BOND : angle 1.06867 / 0.62 ( 10) hydrogen bonds : bond 0.03437 / 2.33 ( 363) hydrogen bonds : angle 4.34123 / 3.16 ( 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 132 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.218 Fit side-chains REVERT: A 173 ARG cc_start: 0.7947 (mtt-85) cc_final: 0.7689 (mtt90) REVERT: A 181 MET cc_start: 0.7915 (mtt) cc_final: 0.7585 (mtp) REVERT: A 291 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.5273 (t80) REVERT: A 424 PHE cc_start: 0.7953 (t80) cc_final: 0.7200 (t80) REVERT: B 60 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: B 153 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7155 (p0) outliers start: 18 outliers final: 14 residues processed: 118 average time/residue: 0.0681 time to fit residues: 10.7344 Evaluate side-chains 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 139 ILE Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 168 MET 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 190 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 chunk 72 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN C 112 ASN C 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.164061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141306 restraints weight = 27517.978| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.76 r_work (final): 0.3675 ------------------------------------------------------------------------------- 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 = 0.22 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 = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.004 0.047 6794 Z= 0.154 Angle : 0.704 13.640 9284 Z= 0.331 Chirality : 0.042 0.153 1112 Planarity : 0.005 0.051 1119 Dihedral : 8.800 58.757 1037 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % 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: -0.07 (0.29), residues: 865 helix: 1.83 (0.27), residues: 377 sheet: -0.46 (0.39), residues: 185 loop : -2.26 (0.33), residues: 303 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 0.024 0.002 PHE A 427 TRP 0.022 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 6789) covalent geometry : angle 0.70388 / 0.33 ( 9274) SS BOND : bond 0.00192 / 0.10 ( 5) SS BOND : angle 1.10377 / 0.64 ( 10) hydrogen bonds : bond 0.03427 / 2.33 ( 363) hydrogen bonds : angle 4.35019 / 3.17 ( 1064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.59 seconds wall clock time: 20 minutes 51.70 seconds (1251.70 seconds total)