Starting phenix.real_space_refine on Sat Dec 28 07:38:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2t_27149/12_2024/8d2t_27149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2t_27149/12_2024/8d2t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2t_27149/12_2024/8d2t_27149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2t_27149/12_2024/8d2t_27149.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2t_27149/12_2024/8d2t_27149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2t_27149/12_2024/8d2t_27149.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.042 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} 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: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} 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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 6, '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: {'GLN:plan1': 1, 'GLU:plan': 2, '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: 6.80, per 1000 atoms: 1.03 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: 1.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... Secondary structure from input PDB file: 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: 0.68 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: 1.95 Time building geometry restraints manager: 1.91 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- 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 6789 Z= 0.729 Angle : 1.101 9.528 9274 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.28), residues: 865 helix: 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 TRP 0.015 0.002 TRP C 33 HIS 0.004 0.002 HIS A 156 PHE 0.029 0.002 PHE C 38 TYR 0.008 0.001 TYR A 251 ARG 0.002 0.000 ARG C 31 *********************** 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 : 0.607 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: 0.6816 (mt0) outliers start: 3 outliers final: 0 residues processed: 151 average time/residue: 0.1970 time to fit residues: 38.7886 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 : 0.677 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 40.0000 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 37 GLN C 50 ASN C 57 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6789 Z= 0.308 Angle : 0.871 11.607 9274 Z= 0.384 Chirality : 0.051 0.297 1112 Planarity : 0.005 0.055 1119 Dihedral : 20.430 82.010 1587 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.29), residues: 865 helix: 1.33 (0.27), residues: 376 sheet: -0.54 (0.40), residues: 179 loop : -2.29 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.025 0.002 PHE C 38 TYR 0.011 0.001 TYR A 159 ARG 0.005 0.001 ARG A 84 *********************** 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: 15 poor density : 124 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7721 (m-80) cc_final: 0.7516 (m-10) REVERT: A 181 MET cc_start: 0.7924 (mtt) cc_final: 0.7613 (mtp) REVERT: A 189 LEU cc_start: 0.8426 (tp) cc_final: 0.8217 (tt) REVERT: A 206 CYS cc_start: 0.5185 (m) cc_final: 0.4633 (m) REVERT: A 291 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.5729 (t80) REVERT: B 60 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.6873 (mt0) REVERT: B 198 MET cc_start: 0.7740 (mmm) cc_final: 0.7157 (mmt) outliers start: 15 outliers final: 6 residues processed: 133 average time/residue: 0.1945 time to fit residues: 34.1160 Evaluate side-chains 118 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 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 238 ASN C 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6789 Z= 0.260 Angle : 0.781 11.559 9274 Z= 0.354 Chirality : 0.048 0.337 1112 Planarity : 0.005 0.054 1119 Dihedral : 14.442 65.269 1587 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.88 % Allowed : 13.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.29), residues: 865 helix: 1.48 (0.27), residues: 376 sheet: -0.62 (0.39), residues: 181 loop : -2.25 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 344 HIS 0.003 0.002 HIS A 288 PHE 0.024 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.006 0.001 ARG B 191 *********************** 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 129 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7876 (mtt) cc_final: 0.7612 (mtp) REVERT: A 291 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6010 (t80) REVERT: B 60 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.6908 (mt0) outliers start: 11 outliers final: 6 residues processed: 124 average time/residue: 0.1942 time to fit residues: 32.0211 Evaluate side-chains 117 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 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 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 77 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6789 Z= 0.240 Angle : 0.742 11.058 9274 Z= 0.339 Chirality : 0.046 0.315 1112 Planarity : 0.005 0.053 1119 Dihedral : 13.028 59.690 1587 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.05 % Allowed : 14.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.29), residues: 865 helix: 1.68 (0.27), residues: 376 sheet: -0.63 (0.39), residues: 181 loop : -2.26 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.024 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.005 0.001 ARG B 191 *********************** 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 131 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7858 (mtt) cc_final: 0.7603 (mtp) REVERT: A 291 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.5294 (t80) REVERT: B 60 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: B 198 MET cc_start: 0.7743 (mmm) cc_final: 0.7340 (mmt) outliers start: 12 outliers final: 9 residues processed: 125 average time/residue: 0.1933 time to fit residues: 31.8714 Evaluate side-chains 124 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6789 Z= 0.271 Angle : 0.738 10.496 9274 Z= 0.344 Chirality : 0.046 0.274 1112 Planarity : 0.005 0.054 1119 Dihedral : 12.138 59.953 1587 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.91 % Allowed : 14.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 865 helix: 1.69 (0.27), residues: 376 sheet: -0.68 (0.38), residues: 187 loop : -2.24 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.025 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.006 0.001 ARG B 191 *********************** 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 133 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.658 Fit side-chains REVERT: A 164 MET cc_start: 0.7558 (mmm) cc_final: 0.7234 (mmm) REVERT: A 173 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7429 (mtt90) REVERT: A 181 MET cc_start: 0.7873 (mtt) cc_final: 0.7619 (mtp) REVERT: A 291 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.5614 (t80) REVERT: B 60 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7146 (mt0) REVERT: B 198 MET cc_start: 0.7772 (mmm) cc_final: 0.7449 (mmt) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 0.1972 time to fit residues: 31.8395 Evaluate side-chains 127 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 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 27 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6789 Z= 0.277 Angle : 0.724 10.608 9274 Z= 0.341 Chirality : 0.045 0.258 1112 Planarity : 0.005 0.055 1119 Dihedral : 11.489 59.832 1587 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.25 % Allowed : 14.73 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 865 helix: 1.75 (0.27), residues: 376 sheet: -0.70 (0.39), residues: 180 loop : -2.25 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.026 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.007 0.001 ARG B 191 *********************** 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 140 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.168 Fit side-chains REVERT: A 164 MET cc_start: 0.7564 (mmm) cc_final: 0.7231 (mmm) REVERT: A 173 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7512 (mtt90) REVERT: A 181 MET cc_start: 0.7868 (mtt) cc_final: 0.7619 (mtp) REVERT: A 291 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.5113 (t80) REVERT: B 60 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: B 198 MET cc_start: 0.7799 (mmm) cc_final: 0.7506 (mmt) outliers start: 19 outliers final: 14 residues processed: 128 average time/residue: 0.2020 time to fit residues: 34.2335 Evaluate side-chains 133 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 257 VAL 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 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 9 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6789 Z= 0.262 Angle : 0.714 10.516 9274 Z= 0.339 Chirality : 0.044 0.203 1112 Planarity : 0.005 0.054 1119 Dihedral : 10.746 59.160 1587 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.42 % Allowed : 15.41 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 865 helix: 1.74 (0.27), residues: 377 sheet: -0.69 (0.39), residues: 180 loop : -2.29 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.026 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.007 0.001 ARG B 191 *********************** 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: 20 poor density : 117 time to evaluate : 0.640 Fit side-chains REVERT: A 173 ARG cc_start: 0.7787 (mtt-85) cc_final: 0.7531 (mtt90) REVERT: A 181 MET cc_start: 0.7861 (mtt) cc_final: 0.7602 (mtp) REVERT: B 60 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: B 198 MET cc_start: 0.7745 (mmm) cc_final: 0.7489 (mmt) outliers start: 20 outliers final: 14 residues processed: 125 average time/residue: 0.1962 time to fit residues: 32.1410 Evaluate side-chains 128 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 190 ILE Chi-restraints excluded: chain A residue 257 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6789 Z= 0.313 Angle : 0.741 10.893 9274 Z= 0.355 Chirality : 0.044 0.184 1112 Planarity : 0.005 0.054 1119 Dihedral : 10.591 59.385 1587 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.77 % Allowed : 15.58 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.29), residues: 865 helix: 1.69 (0.27), residues: 376 sheet: -0.75 (0.41), residues: 163 loop : -2.35 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.028 0.002 PHE C 38 TYR 0.010 0.001 TYR A 251 ARG 0.007 0.001 ARG B 191 *********************** 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: 22 poor density : 113 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7715 (mmm) cc_final: 0.7251 (mmm) REVERT: A 181 MET cc_start: 0.7857 (mtt) cc_final: 0.7590 (mtp) REVERT: A 291 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 60 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: B 198 MET cc_start: 0.7775 (mmm) cc_final: 0.7533 (mmt) outliers start: 22 outliers final: 16 residues processed: 121 average time/residue: 0.2052 time to fit residues: 32.4292 Evaluate side-chains 130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 190 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 40.0000 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 0.0670 chunk 76 optimal weight: 0.1980 chunk 50 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 112 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6789 Z= 0.217 Angle : 0.688 10.082 9274 Z= 0.328 Chirality : 0.042 0.178 1112 Planarity : 0.005 0.054 1119 Dihedral : 10.084 59.882 1587 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.42 % Allowed : 16.27 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.30), residues: 865 helix: 1.85 (0.27), residues: 377 sheet: -0.69 (0.40), residues: 180 loop : -2.31 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.024 0.002 PHE A 427 TYR 0.008 0.001 TYR A 251 ARG 0.007 0.001 ARG B 191 *********************** 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 137 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7771 (mtt) cc_final: 0.7458 (mtp) REVERT: A 291 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6295 (t80) REVERT: A 318 TYR cc_start: 0.8669 (m-80) cc_final: 0.8270 (m-80) REVERT: B 60 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: B 198 MET cc_start: 0.7740 (mmm) cc_final: 0.7518 (mmt) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.1997 time to fit residues: 32.6505 Evaluate side-chains 130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 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 B residue 200 LEU Chi-restraints excluded: chain C residue 112 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 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 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 41 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6789 Z= 0.233 Angle : 0.700 9.636 9274 Z= 0.330 Chirality : 0.043 0.180 1112 Planarity : 0.005 0.053 1119 Dihedral : 9.971 59.908 1587 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.74 % Allowed : 17.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.30), residues: 865 helix: 1.87 (0.27), residues: 376 sheet: -0.66 (0.40), residues: 180 loop : -2.28 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.024 0.002 PHE A 427 TYR 0.009 0.001 TYR A 251 ARG 0.007 0.001 ARG B 191 ********************** 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 130 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.7791 (mtt) cc_final: 0.7465 (mtp) REVERT: A 291 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6454 (t80) REVERT: A 318 TYR cc_start: 0.8688 (m-80) cc_final: 0.8251 (m-80) REVERT: A 424 PHE cc_start: 0.8020 (t80) cc_final: 0.7738 (t80) REVERT: B 60 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: B 198 MET cc_start: 0.7731 (mmm) cc_final: 0.7528 (mmt) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.1897 time to fit residues: 30.3956 Evaluate side-chains 132 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 291 TYR Chi-restraints excluded: chain A residue 303 LEU 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 B residue 200 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 188 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 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.0040 chunk 3 optimal weight: 0.0870 chunk 49 optimal weight: 0.7980 overall best weight: 0.2570 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.168070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.145748 restraints weight = 21151.219| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.31 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 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 = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6789 Z= 0.182 Angle : 0.659 9.476 9274 Z= 0.312 Chirality : 0.041 0.173 1112 Planarity : 0.005 0.054 1119 Dihedral : 9.304 59.645 1587 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.23 % Allowed : 18.15 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.30), residues: 865 helix: 2.04 (0.27), residues: 376 sheet: -0.58 (0.39), residues: 185 loop : -2.23 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.024 0.001 PHE A 427 TYR 0.008 0.001 TYR A 124 ARG 0.007 0.001 ARG B 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.67 seconds wall clock time: 32 minutes 38.45 seconds (1958.45 seconds total)