Starting phenix.real_space_refine on Tue Mar 11 14:30:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyh_21460/03_2025/6vyh_21460.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyh_21460/03_2025/6vyh_21460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vyh_21460/03_2025/6vyh_21460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyh_21460/03_2025/6vyh_21460.map" model { file = "/net/cci-nas-00/data/ceres_data/6vyh_21460/03_2025/6vyh_21460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyh_21460/03_2025/6vyh_21460.cif" } resolution = 3.0 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians Co 2 6.85 5 S 33 5.16 5 C 3898 2.51 5 N 1030 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6093 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3305 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 8, 'TRANS': 419} Chain breaks: 2 Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1348 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1437 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2017 SG CYS A 326 43.574 81.441 42.997 1.00 77.54 S Time building chain proxies: 4.01, per 1000 atoms: 0.66 Number of scatterers: 6093 At special positions: 0 Unit cell: (132.566, 112.514, 83.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Co 2 26.99 S 33 16.00 O 1130 8.00 N 1030 7.00 C 3898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " 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: 1.53 Conformation dependent library (CDL) restraints added in 925.2 milliseconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 25 through 50 removed outlier: 3.710A pdb=" N TYR A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 removed outlier: 5.624A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.543A pdb=" N ALA A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 163 removed outlier: 3.995A pdb=" N TYR A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 199 removed outlier: 3.614A pdb=" N ASN A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Proline residue: A 189 - end of helix removed outlier: 3.579A pdb=" N GLY A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 230 removed outlier: 3.772A pdb=" N CYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.686A pdb=" N ARG A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.505A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.642A pdb=" N THR A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.786A pdb=" N SER A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.533A pdb=" N PHE A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.636A pdb=" N TRP A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 385 through 393 removed outlier: 4.057A pdb=" N VAL A 391 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 removed outlier: 3.601A pdb=" N PHE A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 484 removed outlier: 3.854A pdb=" N LEU A 475 " --> pdb=" O TRP A 471 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 513 removed outlier: 3.593A pdb=" N ASN A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 504 " --> pdb=" O MET A 500 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 removed outlier: 4.421A pdb=" N PHE A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.552A pdb=" N PHE A 540 " --> pdb=" O HIS A 536 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 542 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.524A pdb=" N ARG C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 209' Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.557A pdb=" N TYR D 51 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.799A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 4.154A pdb=" N THR C 117 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.809A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 87 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 3.581A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA6, first strand: chain 'C' and resid 211 through 216 removed outlier: 3.685A pdb=" N TYR C 212 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.491A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.773A pdb=" N VAL D 167 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 195 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR D 201 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 193 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 179 321 hydrogen bonds defined for protein. 897 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: 1.93 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1303 1.33 - 1.45: 1455 1.45 - 1.57: 3390 1.57 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6202 Sorted by residual: bond pdb=" N ILE C 126 " pdb=" CA ILE C 126 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.97e+00 bond pdb=" N GLU C 128 " pdb=" CA GLU C 128 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 9.16e+00 bond pdb=" CA VAL D 208 " pdb=" CB VAL D 208 " ideal model delta sigma weight residual 1.553 1.531 0.022 7.40e-03 1.83e+04 9.05e+00 bond pdb=" N VAL A 341 " pdb=" CA VAL A 341 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.00e+00 bond pdb=" N TYR D 128 " pdb=" CA TYR D 128 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.95e+00 ... (remaining 6197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 7869 2.10 - 4.19: 526 4.19 - 6.29: 48 6.29 - 8.38: 15 8.38 - 10.48: 1 Bond angle restraints: 8459 Sorted by residual: angle pdb=" N PRO D 151 " pdb=" CA PRO D 151 " pdb=" CB PRO D 151 " ideal model delta sigma weight residual 103.25 111.38 -8.13 1.05e+00 9.07e-01 5.99e+01 angle pdb=" N PRO D 192 " pdb=" CA PRO D 192 " pdb=" CB PRO D 192 " ideal model delta sigma weight residual 103.31 109.48 -6.17 8.90e-01 1.26e+00 4.80e+01 angle pdb=" N PRO D 174 " pdb=" CA PRO D 174 " pdb=" CB PRO D 174 " ideal model delta sigma weight residual 103.25 110.32 -7.07 1.05e+00 9.07e-01 4.54e+01 angle pdb=" N PRO D 237 " pdb=" CA PRO D 237 " pdb=" CB PRO D 237 " ideal model delta sigma weight residual 103.25 110.21 -6.96 1.05e+00 9.07e-01 4.39e+01 angle pdb=" N PRO D 144 " pdb=" CA PRO D 144 " pdb=" CB PRO D 144 " ideal model delta sigma weight residual 102.85 110.34 -7.49 1.13e+00 7.83e-01 4.39e+01 ... (remaining 8454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 3225 17.08 - 34.16: 299 34.16 - 51.24: 64 51.24 - 68.32: 3 68.32 - 85.41: 9 Dihedral angle restraints: 3600 sinusoidal: 1139 harmonic: 2461 Sorted by residual: dihedral pdb=" CA GLY D 27 " pdb=" C GLY D 27 " pdb=" N ALA D 28 " pdb=" CA ALA D 28 " ideal model delta harmonic sigma weight residual 180.00 155.84 24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C THR A 334 " pdb=" N THR A 334 " pdb=" CA THR A 334 " pdb=" CB THR A 334 " ideal model delta harmonic sigma weight residual -122.00 -133.98 11.98 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" CA TRP A 127 " pdb=" C TRP A 127 " pdb=" N VAL A 128 " pdb=" CA VAL A 128 " ideal model delta harmonic sigma weight residual -180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 796 0.072 - 0.144: 181 0.144 - 0.216: 23 0.216 - 0.287: 7 0.287 - 0.359: 2 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA THR A 334 " pdb=" N THR A 334 " pdb=" C THR A 334 " pdb=" CB THR A 334 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA TYR D 121 " pdb=" N TYR D 121 " pdb=" C TYR D 121 " pdb=" CB TYR D 121 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE A 513 " pdb=" N ILE A 513 " pdb=" C ILE A 513 " pdb=" CB ILE A 513 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1006 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 512 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C VAL A 512 " -0.061 2.00e-02 2.50e+03 pdb=" O VAL A 512 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 513 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 155 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C GLN A 155 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN A 155 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 156 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 63 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO C 64 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.031 5.00e-02 4.00e+02 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 29 2.52 - 3.11: 4569 3.11 - 3.71: 8663 3.71 - 4.30: 12478 4.30 - 4.90: 21677 Nonbonded interactions: 47416 Sorted by model distance: nonbonded pdb=" OD2 ASP A 39 " pdb="CO CO A 601 " model vdw 1.922 2.220 nonbonded pdb=" SG CYS A 326 " pdb="CO CO A 602 " model vdw 2.112 2.580 nonbonded pdb=" OD1 ASP A 39 " pdb="CO CO A 601 " model vdw 2.141 2.220 nonbonded pdb=" O GLY A 368 " pdb=" OG1 THR A 372 " model vdw 2.215 3.040 nonbonded pdb=" OG SER A 376 " pdb=" OG SER A 472 " model vdw 2.236 3.040 ... (remaining 47411 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=1.00 max=1.00 mean=1.00 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.330 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.013 0.086 6202 Z= 0.829 Angle : 1.112 10.479 8459 Z= 0.707 Chirality : 0.064 0.359 1009 Planarity : 0.005 0.056 1072 Dihedral : 14.405 85.406 2020 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 1.18 % Allowed : 8.82 % Favored : 90.00 % Rotamer: Outliers : 2.00 % Allowed : 10.71 % Favored : 87.30 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % 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: -4.54 (0.24), residues: 850 helix: -3.32 (0.20), residues: 354 sheet: -1.58 (0.36), residues: 188 loop : -3.29 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 69 HIS 0.007 0.002 HIS A 508 PHE 0.021 0.003 PHE D 126 TYR 0.021 0.003 TYR A 220 ARG 0.015 0.002 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.688 Fit side-chains REVERT: A 112 MET cc_start: 0.6879 (mtp) cc_final: 0.6285 (mtt) REVERT: A 195 ILE cc_start: 0.7868 (mm) cc_final: 0.7656 (mm) REVERT: A 538 MET cc_start: 0.8818 (mtp) cc_final: 0.8392 (mtp) REVERT: C 123 LYS cc_start: 0.8010 (tttp) cc_final: 0.7677 (tmtt) REVERT: C 128 GLU cc_start: 0.6730 (tt0) cc_final: 0.5650 (pm20) REVERT: D 106 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8634 (m) outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 0.9975 time to fit residues: 141.0129 Evaluate side-chains 105 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 134 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 86 ASN A 497 GLN C 26 GLN C 73 ASN D 25 GLN D 62 GLN D 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.172140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132218 restraints weight = 6600.172| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.34 r_work: 0.3189 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6202 Z= 0.199 Angle : 0.630 10.522 8459 Z= 0.328 Chirality : 0.042 0.142 1009 Planarity : 0.005 0.065 1072 Dihedral : 5.607 35.521 919 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.71 % Favored : 94.82 % Rotamer: Outliers : 3.99 % Allowed : 20.15 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.27), residues: 850 helix: -1.69 (0.25), residues: 365 sheet: -1.14 (0.36), residues: 194 loop : -2.72 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 69 HIS 0.002 0.001 HIS D 54 PHE 0.011 0.001 PHE D 126 TYR 0.013 0.001 TYR A 133 ARG 0.009 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.632 Fit side-chains REVERT: A 112 MET cc_start: 0.6867 (mtp) cc_final: 0.6398 (mtt) REVERT: A 195 ILE cc_start: 0.7552 (mm) cc_final: 0.6992 (mp) REVERT: A 393 MET cc_start: 0.0477 (ptt) cc_final: -0.0375 (mmt) REVERT: A 507 LEU cc_start: 0.8186 (tp) cc_final: 0.7593 (mt) REVERT: A 538 MET cc_start: 0.9113 (mtp) cc_final: 0.8859 (mtp) REVERT: C 48 ASN cc_start: 0.7998 (t0) cc_final: 0.7633 (t0) REVERT: C 123 LYS cc_start: 0.8306 (tttp) cc_final: 0.7678 (tmtt) REVERT: C 125 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6948 (pt0) REVERT: D 106 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7251 (m) REVERT: D 109 ASP cc_start: 0.8613 (m-30) cc_final: 0.8164 (m-30) outliers start: 22 outliers final: 7 residues processed: 118 average time/residue: 0.9255 time to fit residues: 115.7409 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 23 optimal weight: 0.0060 chunk 26 optimal weight: 0.0370 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.169464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128928 restraints weight = 6730.870| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.23 r_work: 0.3204 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6202 Z= 0.145 Angle : 0.539 8.585 8459 Z= 0.279 Chirality : 0.040 0.147 1009 Planarity : 0.004 0.060 1072 Dihedral : 4.712 37.701 912 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.35 % Favored : 95.18 % Rotamer: Outliers : 3.27 % Allowed : 23.41 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.29), residues: 850 helix: -0.51 (0.28), residues: 358 sheet: -0.67 (0.36), residues: 200 loop : -2.06 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.001 0.000 HIS D 54 PHE 0.010 0.001 PHE C 107 TYR 0.015 0.001 TYR A 502 ARG 0.006 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.679 Fit side-chains REVERT: A 112 MET cc_start: 0.6752 (mtp) cc_final: 0.6292 (mtt) REVERT: A 195 ILE cc_start: 0.7565 (mm) cc_final: 0.7049 (mp) REVERT: A 229 LYS cc_start: 0.7705 (mtpp) cc_final: 0.7489 (mttt) REVERT: A 393 MET cc_start: 0.0650 (ptt) cc_final: 0.0002 (mmt) REVERT: A 507 LEU cc_start: 0.7825 (tp) cc_final: 0.7375 (mt) REVERT: A 538 MET cc_start: 0.9065 (mtp) cc_final: 0.8865 (mtp) REVERT: C 32 SER cc_start: 0.8640 (p) cc_final: 0.8344 (t) REVERT: C 38 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8269 (ttt-90) REVERT: C 123 LYS cc_start: 0.8340 (tttp) cc_final: 0.7742 (tmtt) REVERT: C 125 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: D 131 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7935 (pm20) outliers start: 18 outliers final: 7 residues processed: 110 average time/residue: 0.9960 time to fit residues: 115.8342 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 131 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.167933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125687 restraints weight = 6842.141| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.82 r_work: 0.3193 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6202 Z= 0.171 Angle : 0.528 8.327 8459 Z= 0.274 Chirality : 0.040 0.144 1009 Planarity : 0.004 0.060 1072 Dihedral : 4.229 16.617 908 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.59 % Favored : 94.94 % Rotamer: Outliers : 5.26 % Allowed : 22.69 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.30), residues: 850 helix: -0.04 (0.29), residues: 356 sheet: -0.42 (0.36), residues: 194 loop : -1.82 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.001 0.000 HIS A 43 PHE 0.010 0.001 PHE C 107 TYR 0.010 0.001 TYR A 133 ARG 0.004 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.621 Fit side-chains REVERT: A 112 MET cc_start: 0.6821 (mtp) cc_final: 0.6433 (mtt) REVERT: A 195 ILE cc_start: 0.7672 (mm) cc_final: 0.7104 (mt) REVERT: A 296 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6631 (mmp-170) REVERT: A 324 PHE cc_start: 0.7930 (t80) cc_final: 0.7695 (t80) REVERT: A 393 MET cc_start: 0.0555 (ptt) cc_final: -0.0004 (mmt) REVERT: A 538 MET cc_start: 0.9084 (mtp) cc_final: 0.8803 (mtp) REVERT: C 32 SER cc_start: 0.8651 (p) cc_final: 0.8373 (t) REVERT: C 38 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8181 (ttt-90) REVERT: C 123 LYS cc_start: 0.8275 (tttp) cc_final: 0.7635 (tmtt) REVERT: C 125 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6890 (pt0) REVERT: C 128 GLU cc_start: 0.7110 (tt0) cc_final: 0.4715 (pm20) REVERT: D 131 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7989 (pm20) outliers start: 29 outliers final: 13 residues processed: 112 average time/residue: 0.9791 time to fit residues: 116.1184 Evaluate side-chains 106 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 131 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.0970 chunk 53 optimal weight: 20.0000 chunk 52 optimal weight: 0.0970 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125208 restraints weight = 6707.891| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.70 r_work: 0.3211 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6202 Z= 0.164 Angle : 0.535 8.606 8459 Z= 0.271 Chirality : 0.041 0.144 1009 Planarity : 0.004 0.060 1072 Dihedral : 4.132 16.208 908 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.35 % Favored : 95.18 % Rotamer: Outliers : 5.08 % Allowed : 23.77 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.91 (0.30), residues: 850 helix: 0.16 (0.29), residues: 364 sheet: -0.18 (0.36), residues: 194 loop : -1.76 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.001 0.000 HIS A 508 PHE 0.010 0.001 PHE C 107 TYR 0.010 0.001 TYR A 502 ARG 0.004 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.607 Fit side-chains REVERT: A 112 MET cc_start: 0.6809 (mtp) cc_final: 0.6462 (mtt) REVERT: A 195 ILE cc_start: 0.7745 (mm) cc_final: 0.7385 (mm) REVERT: A 296 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6726 (mmp-170) REVERT: A 324 PHE cc_start: 0.7955 (t80) cc_final: 0.7660 (t80) REVERT: A 393 MET cc_start: 0.0413 (ptt) cc_final: -0.0053 (mmt) REVERT: A 507 LEU cc_start: 0.7798 (tt) cc_final: 0.7208 (mt) REVERT: A 538 MET cc_start: 0.9058 (mtp) cc_final: 0.8726 (mtp) REVERT: C 32 SER cc_start: 0.8601 (p) cc_final: 0.8329 (t) REVERT: C 120 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8606 (m) REVERT: C 123 LYS cc_start: 0.8225 (tttp) cc_final: 0.7602 (tmtt) REVERT: C 125 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6903 (pt0) REVERT: C 128 GLU cc_start: 0.7232 (tt0) cc_final: 0.4796 (pm20) outliers start: 28 outliers final: 15 residues processed: 110 average time/residue: 0.9640 time to fit residues: 112.4017 Evaluate side-chains 114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 18 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123944 restraints weight = 6658.433| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.85 r_work: 0.3199 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6202 Z= 0.172 Angle : 0.537 11.702 8459 Z= 0.271 Chirality : 0.040 0.145 1009 Planarity : 0.004 0.059 1072 Dihedral : 4.066 16.033 908 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.59 % Favored : 94.94 % Rotamer: Outliers : 4.90 % Allowed : 24.68 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.72 (0.30), residues: 850 helix: 0.32 (0.29), residues: 368 sheet: -0.08 (0.36), residues: 203 loop : -1.76 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 127 HIS 0.001 0.000 HIS A 536 PHE 0.010 0.001 PHE A 44 TYR 0.016 0.001 TYR A 133 ARG 0.006 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.672 Fit side-chains REVERT: A 112 MET cc_start: 0.6565 (mtp) cc_final: 0.6267 (mtt) REVERT: A 195 ILE cc_start: 0.7749 (mm) cc_final: 0.7350 (mm) REVERT: A 296 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6650 (mmp-170) REVERT: A 324 PHE cc_start: 0.8155 (t80) cc_final: 0.7859 (t80) REVERT: A 389 ILE cc_start: 0.7691 (tp) cc_final: 0.7452 (tp) REVERT: A 393 MET cc_start: 0.0457 (ptt) cc_final: -0.0082 (mmt) REVERT: A 507 LEU cc_start: 0.7717 (tt) cc_final: 0.7162 (mt) REVERT: A 523 LEU cc_start: 0.7612 (mm) cc_final: 0.7281 (tp) REVERT: A 530 SER cc_start: 0.8445 (m) cc_final: 0.8130 (m) REVERT: A 538 MET cc_start: 0.9079 (mtp) cc_final: 0.8670 (mtp) REVERT: C 32 SER cc_start: 0.8589 (p) cc_final: 0.8383 (t) REVERT: C 38 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.7746 (ttp80) REVERT: C 120 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8617 (m) REVERT: C 123 LYS cc_start: 0.8224 (tttp) cc_final: 0.7575 (tmtt) REVERT: C 125 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6872 (pt0) REVERT: C 128 GLU cc_start: 0.7236 (tt0) cc_final: 0.4867 (pm20) outliers start: 27 outliers final: 19 residues processed: 120 average time/residue: 0.9564 time to fit residues: 121.4526 Evaluate side-chains 125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121775 restraints weight = 6819.825| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.84 r_work: 0.3169 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6202 Z= 0.223 Angle : 0.569 11.347 8459 Z= 0.286 Chirality : 0.041 0.144 1009 Planarity : 0.004 0.061 1072 Dihedral : 4.157 16.680 908 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.94 % Favored : 94.59 % Rotamer: Outliers : 5.08 % Allowed : 25.95 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.30), residues: 850 helix: 0.40 (0.29), residues: 362 sheet: -0.04 (0.37), residues: 198 loop : -1.71 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.001 0.000 HIS D 54 PHE 0.012 0.001 PHE D 126 TYR 0.027 0.002 TYR A 133 ARG 0.005 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.676 Fit side-chains REVERT: A 195 ILE cc_start: 0.7791 (mm) cc_final: 0.7405 (mm) REVERT: A 296 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6689 (mmp-170) REVERT: A 319 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7809 (tpp) REVERT: A 324 PHE cc_start: 0.8112 (t80) cc_final: 0.7834 (t80) REVERT: A 389 ILE cc_start: 0.7709 (tp) cc_final: 0.7460 (tp) REVERT: A 393 MET cc_start: 0.0485 (ptt) cc_final: -0.0151 (mmt) REVERT: A 507 LEU cc_start: 0.7789 (tt) cc_final: 0.7241 (mt) REVERT: A 530 SER cc_start: 0.8475 (m) cc_final: 0.8154 (m) REVERT: C 32 SER cc_start: 0.8604 (p) cc_final: 0.8403 (t) REVERT: C 48 ASN cc_start: 0.8210 (t0) cc_final: 0.7779 (t0) REVERT: C 120 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8637 (m) REVERT: C 123 LYS cc_start: 0.8262 (tttp) cc_final: 0.7596 (tmtt) REVERT: C 125 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6805 (pt0) REVERT: C 128 GLU cc_start: 0.7262 (tt0) cc_final: 0.4850 (pm20) outliers start: 28 outliers final: 18 residues processed: 118 average time/residue: 0.9641 time to fit residues: 120.6019 Evaluate side-chains 125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.164583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123527 restraints weight = 6747.549| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.74 r_work: 0.3166 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6202 Z= 0.219 Angle : 0.567 11.379 8459 Z= 0.284 Chirality : 0.041 0.144 1009 Planarity : 0.004 0.063 1072 Dihedral : 4.155 16.760 908 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.94 % Favored : 94.59 % Rotamer: Outliers : 4.90 % Allowed : 26.32 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.60 (0.30), residues: 850 helix: 0.45 (0.29), residues: 363 sheet: 0.07 (0.36), residues: 204 loop : -1.78 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.002 0.000 HIS D 54 PHE 0.011 0.001 PHE D 126 TYR 0.034 0.002 TYR A 133 ARG 0.007 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.703 Fit side-chains REVERT: A 53 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7131 (tt) REVERT: A 195 ILE cc_start: 0.7766 (mm) cc_final: 0.7400 (mm) REVERT: A 296 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6874 (mmp-170) REVERT: A 324 PHE cc_start: 0.8183 (t80) cc_final: 0.7853 (t80) REVERT: A 389 ILE cc_start: 0.7676 (tp) cc_final: 0.7419 (tp) REVERT: A 393 MET cc_start: 0.0494 (ptt) cc_final: -0.0393 (mmt) REVERT: A 523 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7260 (tp) REVERT: A 530 SER cc_start: 0.8431 (m) cc_final: 0.8106 (m) REVERT: C 48 ASN cc_start: 0.8232 (t0) cc_final: 0.7802 (t0) REVERT: C 120 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8634 (m) REVERT: C 123 LYS cc_start: 0.8352 (tttp) cc_final: 0.7683 (tmtt) REVERT: C 125 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6828 (pt0) outliers start: 27 outliers final: 18 residues processed: 116 average time/residue: 0.9412 time to fit residues: 115.6823 Evaluate side-chains 126 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120737 restraints weight = 6730.608| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.77 r_work: 0.3139 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6202 Z= 0.272 Angle : 0.606 11.541 8459 Z= 0.304 Chirality : 0.043 0.190 1009 Planarity : 0.004 0.065 1072 Dihedral : 4.319 17.420 908 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.06 % Favored : 94.47 % Rotamer: Outliers : 5.63 % Allowed : 25.95 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.63 (0.30), residues: 850 helix: 0.32 (0.28), residues: 364 sheet: 0.19 (0.37), residues: 196 loop : -1.71 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS D 54 PHE 0.013 0.001 PHE D 126 TYR 0.037 0.002 TYR A 133 ARG 0.008 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.695 Fit side-chains REVERT: A 195 ILE cc_start: 0.7732 (mm) cc_final: 0.7382 (mm) REVERT: A 296 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7019 (mmt180) REVERT: A 324 PHE cc_start: 0.8221 (t80) cc_final: 0.7959 (t80) REVERT: A 389 ILE cc_start: 0.7566 (tp) cc_final: 0.7321 (tp) REVERT: A 393 MET cc_start: 0.0391 (ptt) cc_final: -0.0534 (mmt) REVERT: A 530 SER cc_start: 0.8432 (m) cc_final: 0.8127 (m) REVERT: C 48 ASN cc_start: 0.8355 (t0) cc_final: 0.7872 (t0) REVERT: C 123 LYS cc_start: 0.8424 (tttp) cc_final: 0.7709 (tmtt) REVERT: C 125 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6801 (pt0) REVERT: C 127 LYS cc_start: 0.8264 (ttpt) cc_final: 0.8017 (ttmt) outliers start: 31 outliers final: 22 residues processed: 118 average time/residue: 0.9512 time to fit residues: 119.0196 Evaluate side-chains 125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 57 optimal weight: 40.0000 chunk 5 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122784 restraints weight = 6786.625| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.88 r_work: 0.3186 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6202 Z= 0.186 Angle : 0.575 14.329 8459 Z= 0.282 Chirality : 0.041 0.144 1009 Planarity : 0.004 0.065 1072 Dihedral : 4.181 21.474 908 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.59 % Favored : 94.94 % Rotamer: Outliers : 4.72 % Allowed : 26.68 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.30), residues: 850 helix: 0.52 (0.29), residues: 365 sheet: 0.28 (0.37), residues: 202 loop : -1.75 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 69 HIS 0.002 0.001 HIS A 508 PHE 0.010 0.001 PHE A 44 TYR 0.038 0.001 TYR A 133 ARG 0.008 0.001 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.606 Fit side-chains REVERT: A 195 ILE cc_start: 0.7722 (mm) cc_final: 0.7357 (mm) REVERT: A 296 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7076 (mmt180) REVERT: A 324 PHE cc_start: 0.8131 (t80) cc_final: 0.7850 (t80) REVERT: A 389 ILE cc_start: 0.7619 (tp) cc_final: 0.7376 (tp) REVERT: A 393 MET cc_start: 0.0409 (ptt) cc_final: -0.0448 (mmt) REVERT: A 507 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7446 (pp) REVERT: A 530 SER cc_start: 0.8432 (m) cc_final: 0.8110 (m) REVERT: C 29 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8051 (mtpm) REVERT: C 48 ASN cc_start: 0.8258 (t0) cc_final: 0.7822 (t0) REVERT: C 120 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8646 (m) REVERT: C 123 LYS cc_start: 0.8373 (tttp) cc_final: 0.7708 (tmtt) REVERT: C 125 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6955 (pt0) outliers start: 26 outliers final: 14 residues processed: 113 average time/residue: 0.9793 time to fit residues: 117.1840 Evaluate side-chains 121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 overall best weight: 0.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122899 restraints weight = 6809.045| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.80 r_work: 0.3172 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6202 Z= 0.181 Angle : 0.570 12.596 8459 Z= 0.281 Chirality : 0.041 0.142 1009 Planarity : 0.004 0.064 1072 Dihedral : 4.158 20.395 908 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.06 % Favored : 94.59 % Rotamer: Outliers : 3.63 % Allowed : 27.77 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.30), residues: 850 helix: 0.62 (0.29), residues: 365 sheet: 0.40 (0.38), residues: 202 loop : -1.69 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.001 0.000 HIS A 536 PHE 0.015 0.001 PHE A 49 TYR 0.038 0.001 TYR A 133 ARG 0.008 0.001 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5470.49 seconds wall clock time: 93 minutes 37.44 seconds (5617.44 seconds total)