Starting phenix.real_space_refine on Fri Dec 27 17:00:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vyh_21460/12_2024/6vyh_21460.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyh_21460/12_2024/6vyh_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_21460/12_2024/6vyh_21460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyh_21460/12_2024/6vyh_21460.map" model { file = "/net/cci-nas-00/data/ceres_data/6vyh_21460/12_2024/6vyh_21460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyh_21460/12_2024/6vyh_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-5532/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: 4.04, 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: 1.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.71 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: 1.86 Time building geometry restraints manager: 1.81 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: 0.510 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: 0.050 Set scattering table: 0.060 Process input model: 18.090 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- 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 : 0.672 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: 1.0128 time to fit residues: 143.2952 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 : 0.713 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.636 Fit side-chains REVERT: A 112 MET cc_start: 0.6650 (mtp) cc_final: 0.6141 (mtt) REVERT: A 195 ILE cc_start: 0.7618 (mm) cc_final: 0.7142 (mp) REVERT: A 393 MET cc_start: 0.0582 (ptt) cc_final: -0.0302 (mmt) REVERT: A 507 LEU cc_start: 0.8155 (tp) cc_final: 0.7743 (mt) REVERT: A 538 MET cc_start: 0.8687 (mtp) cc_final: 0.8428 (mtp) REVERT: C 32 SER cc_start: 0.8415 (t) cc_final: 0.8123 (p) REVERT: C 123 LYS cc_start: 0.7935 (tttp) cc_final: 0.7584 (tmtt) REVERT: C 125 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6777 (pt0) REVERT: D 106 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7746 (m) REVERT: D 109 ASP cc_start: 0.8424 (m-30) cc_final: 0.8013 (m-30) outliers start: 22 outliers final: 7 residues processed: 118 average time/residue: 1.0182 time to fit residues: 127.6436 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 : 0.865 ------------------------------------------------------------------------------- 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 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.0000 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 30.0000 chunk 82 optimal weight: 0.4980 chunk 68 optimal weight: 0.0870 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 61 optimal weight: 40.0000 overall best weight: 0.4562 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2640 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= 0.147 Angle : 0.543 8.710 8459 Z= 0.281 Chirality : 0.040 0.146 1009 Planarity : 0.004 0.060 1072 Dihedral : 4.751 37.649 912 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.59 % Favored : 94.94 % 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: -1.82 (0.29), residues: 850 helix: -0.62 (0.28), residues: 363 sheet: -0.73 (0.36), residues: 198 loop : -2.14 (0.37), residues: 289 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 : 0.686 Fit side-chains REVERT: A 112 MET cc_start: 0.6530 (mtp) cc_final: 0.6037 (mtt) REVERT: A 173 MET cc_start: 0.8235 (mtt) cc_final: 0.7956 (mtm) REVERT: A 195 ILE cc_start: 0.7654 (mm) cc_final: 0.7157 (mp) REVERT: A 393 MET cc_start: 0.0712 (ptt) cc_final: 0.0042 (mmt) REVERT: A 507 LEU cc_start: 0.7666 (tp) cc_final: 0.7448 (mt) REVERT: A 538 MET cc_start: 0.8641 (mtp) cc_final: 0.8430 (mtp) REVERT: C 38 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.8106 (ttt-90) REVERT: C 123 LYS cc_start: 0.7914 (tttp) cc_final: 0.7570 (tmtt) REVERT: C 125 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6802 (pt0) outliers start: 18 outliers final: 7 residues processed: 111 average time/residue: 1.1088 time to fit residues: 129.9583 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 489 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 51 optimal weight: 0.0000 chunk 76 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6202 Z= 0.240 Angle : 0.573 8.797 8459 Z= 0.297 Chirality : 0.042 0.145 1009 Planarity : 0.004 0.061 1072 Dihedral : 4.417 17.446 908 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.71 % Favored : 94.82 % Rotamer: Outliers : 6.35 % Allowed : 21.60 % 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: -1.43 (0.30), residues: 850 helix: -0.38 (0.28), residues: 368 sheet: -0.40 (0.37), residues: 194 loop : -1.92 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.002 0.001 HIS D 54 PHE 0.013 0.001 PHE D 126 TYR 0.011 0.002 TYR A 220 ARG 0.004 0.001 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 134 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.690 Fit side-chains REVERT: A 112 MET cc_start: 0.6587 (mtp) cc_final: 0.6145 (mtt) REVERT: A 173 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8071 (mtm) REVERT: A 195 ILE cc_start: 0.7788 (mm) cc_final: 0.7319 (mt) REVERT: A 296 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6627 (mmp-170) REVERT: A 324 PHE cc_start: 0.7988 (t80) cc_final: 0.7760 (t80) REVERT: A 393 MET cc_start: 0.0845 (ptt) cc_final: 0.0123 (mmt) REVERT: A 507 LEU cc_start: 0.7896 (tp) cc_final: 0.7671 (mt) REVERT: A 538 MET cc_start: 0.8716 (mtp) cc_final: 0.8257 (mtp) REVERT: C 123 LYS cc_start: 0.7920 (tttp) cc_final: 0.7524 (tmtt) REVERT: C 125 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6772 (pt0) REVERT: C 127 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7813 (ttmt) REVERT: C 128 GLU cc_start: 0.7037 (tt0) cc_final: 0.5695 (pm20) outliers start: 35 outliers final: 17 residues processed: 118 average time/residue: 1.0203 time to fit residues: 127.2947 Evaluate side-chains 112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 215 SER 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 29 LYS 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 93 THR Chi-restraints excluded: chain D residue 117 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6202 Z= 0.267 Angle : 0.582 8.789 8459 Z= 0.300 Chirality : 0.042 0.147 1009 Planarity : 0.004 0.065 1072 Dihedral : 4.467 17.342 908 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.94 % Favored : 94.59 % Rotamer: Outliers : 5.99 % Allowed : 23.96 % Favored : 70.05 % 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: -1.17 (0.30), residues: 850 helix: -0.12 (0.28), residues: 362 sheet: -0.32 (0.37), residues: 196 loop : -1.79 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.002 0.001 HIS D 54 PHE 0.013 0.001 PHE D 126 TYR 0.011 0.002 TYR A 220 ARG 0.005 0.001 ARG C 38 *********************** 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 139 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.672 Fit side-chains REVERT: A 112 MET cc_start: 0.6538 (mtp) cc_final: 0.6126 (mtt) REVERT: A 195 ILE cc_start: 0.7814 (mm) cc_final: 0.7507 (mm) REVERT: A 296 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7190 (mmt180) REVERT: A 324 PHE cc_start: 0.8209 (t80) cc_final: 0.7900 (t80) REVERT: A 393 MET cc_start: 0.0263 (ptt) cc_final: -0.0310 (mmt) REVERT: A 530 SER cc_start: 0.8312 (m) cc_final: 0.7973 (m) REVERT: A 538 MET cc_start: 0.8688 (mtp) cc_final: 0.8231 (mtp) REVERT: C 123 LYS cc_start: 0.8045 (tttp) cc_final: 0.7603 (tmtt) REVERT: C 125 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6764 (pt0) REVERT: C 127 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7877 (ttmt) REVERT: C 128 GLU cc_start: 0.7203 (tt0) cc_final: 0.5770 (pm20) outliers start: 33 outliers final: 17 residues processed: 125 average time/residue: 1.0122 time to fit residues: 133.7216 Evaluate side-chains 118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 215 SER 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 34 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6202 Z= 0.239 Angle : 0.566 8.725 8459 Z= 0.292 Chirality : 0.042 0.145 1009 Planarity : 0.004 0.065 1072 Dihedral : 4.358 17.151 908 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.94 % Favored : 94.59 % Rotamer: Outliers : 5.81 % Allowed : 25.05 % Favored : 69.15 % 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: -1.01 (0.30), residues: 850 helix: 0.04 (0.28), residues: 363 sheet: -0.19 (0.37), residues: 196 loop : -1.80 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.002 0.000 HIS D 54 PHE 0.012 0.001 PHE D 126 TYR 0.017 0.002 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 136 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.668 Fit side-chains REVERT: A 112 MET cc_start: 0.6491 (mtp) cc_final: 0.6090 (mtt) REVERT: A 195 ILE cc_start: 0.7789 (mm) cc_final: 0.7488 (mm) REVERT: A 296 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6956 (mmt180) REVERT: A 393 MET cc_start: 0.0165 (ptt) cc_final: -0.0408 (mmt) REVERT: A 530 SER cc_start: 0.8305 (m) cc_final: 0.7969 (m) REVERT: A 538 MET cc_start: 0.8629 (mtp) cc_final: 0.8357 (mtp) REVERT: C 123 LYS cc_start: 0.8072 (tttp) cc_final: 0.7595 (tmtt) REVERT: C 125 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6770 (pt0) REVERT: C 127 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7865 (ttmt) REVERT: C 128 GLU cc_start: 0.7152 (tt0) cc_final: 0.5741 (pm20) outliers start: 32 outliers final: 21 residues processed: 122 average time/residue: 1.0358 time to fit residues: 133.5012 Evaluate side-chains 124 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 102 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 215 SER 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 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 34 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6202 Z= 0.233 Angle : 0.563 8.989 8459 Z= 0.288 Chirality : 0.042 0.145 1009 Planarity : 0.004 0.065 1072 Dihedral : 4.303 16.819 908 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.18 % Favored : 94.35 % Rotamer: Outliers : 5.99 % Allowed : 25.41 % 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: -0.84 (0.30), residues: 850 helix: 0.14 (0.28), residues: 366 sheet: -0.06 (0.37), residues: 196 loop : -1.71 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.002 0.000 HIS D 54 PHE 0.012 0.001 PHE D 126 TYR 0.025 0.002 TYR A 133 ARG 0.006 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 136 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.652 Fit side-chains REVERT: A 195 ILE cc_start: 0.7801 (mm) cc_final: 0.7466 (mm) REVERT: A 296 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6960 (mmt180) REVERT: A 393 MET cc_start: 0.0460 (ptt) cc_final: -0.0353 (mmt) REVERT: A 530 SER cc_start: 0.8332 (m) cc_final: 0.7977 (m) REVERT: A 538 MET cc_start: 0.8686 (mtp) cc_final: 0.8226 (mtp) REVERT: C 85 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7924 (m) REVERT: C 123 LYS cc_start: 0.8066 (tttp) cc_final: 0.7582 (tmtt) REVERT: C 125 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6862 (pt0) REVERT: C 127 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7795 (ttmt) outliers start: 33 outliers final: 22 residues processed: 123 average time/residue: 0.9947 time to fit residues: 129.6687 Evaluate side-chains 127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 102 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 215 SER 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 34 SER 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 85 SER Chi-restraints excluded: chain C residue 107 PHE 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 48 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6202 Z= 0.175 Angle : 0.538 8.676 8459 Z= 0.273 Chirality : 0.041 0.144 1009 Planarity : 0.004 0.065 1072 Dihedral : 4.143 16.217 908 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.82 % Favored : 94.71 % Rotamer: Outliers : 3.99 % Allowed : 27.77 % Favored : 68.24 % 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: -0.56 (0.30), residues: 850 helix: 0.40 (0.29), residues: 366 sheet: 0.12 (0.38), residues: 196 loop : -1.64 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 69 HIS 0.001 0.000 HIS D 54 PHE 0.010 0.001 PHE A 44 TYR 0.034 0.001 TYR A 133 ARG 0.008 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 127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.638 Fit side-chains REVERT: A 195 ILE cc_start: 0.7771 (mm) cc_final: 0.7435 (mm) REVERT: A 296 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6976 (mmt180) REVERT: A 393 MET cc_start: 0.0504 (ptt) cc_final: -0.0274 (mmt) REVERT: A 530 SER cc_start: 0.8320 (m) cc_final: 0.7946 (m) REVERT: A 538 MET cc_start: 0.8643 (mtp) cc_final: 0.8236 (mtp) REVERT: C 29 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8129 (mtpm) REVERT: C 120 SER cc_start: 0.8424 (t) cc_final: 0.8151 (m) REVERT: C 123 LYS cc_start: 0.8026 (tttp) cc_final: 0.7575 (tmtt) REVERT: C 125 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6848 (pt0) REVERT: C 127 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7776 (ttmt) outliers start: 22 outliers final: 14 residues processed: 116 average time/residue: 0.9705 time to fit residues: 119.6078 Evaluate side-chains 118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 215 SER 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 523 LEU Chi-restraints excluded: chain A residue 524 LEU 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 125 GLU 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 75 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6202 Z= 0.251 Angle : 0.572 8.559 8459 Z= 0.292 Chirality : 0.042 0.145 1009 Planarity : 0.004 0.064 1072 Dihedral : 4.265 16.826 908 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.06 % Favored : 94.47 % Rotamer: Outliers : 4.90 % Allowed : 27.22 % Favored : 67.88 % 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: -0.57 (0.30), residues: 850 helix: 0.35 (0.28), residues: 365 sheet: 0.19 (0.38), residues: 196 loop : -1.65 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.002 0.001 HIS D 54 PHE 0.012 0.001 PHE D 126 TYR 0.038 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 128 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.711 Fit side-chains REVERT: A 195 ILE cc_start: 0.7762 (mm) cc_final: 0.7447 (mm) REVERT: A 296 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7008 (mmt180) REVERT: A 393 MET cc_start: 0.0506 (ptt) cc_final: -0.0282 (mmt) REVERT: A 507 LEU cc_start: 0.8032 (mt) cc_final: 0.7732 (tt) REVERT: A 530 SER cc_start: 0.8331 (m) cc_final: 0.7984 (m) REVERT: A 538 MET cc_start: 0.8697 (mtp) cc_final: 0.8228 (mtp) REVERT: C 29 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8117 (mtpm) REVERT: C 85 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7937 (m) REVERT: C 123 LYS cc_start: 0.8070 (tttp) cc_final: 0.7586 (tmtt) REVERT: C 125 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6863 (pt0) REVERT: C 127 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7771 (ttmt) REVERT: D 24 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7637 (mm-40) outliers start: 27 outliers final: 18 residues processed: 117 average time/residue: 0.9848 time to fit residues: 121.9162 Evaluate side-chains 121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 215 SER 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 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 85 SER Chi-restraints excluded: chain C residue 107 PHE 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 37 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 0.0050 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3667 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= 0.213 Angle : 0.562 8.484 8459 Z= 0.284 Chirality : 0.041 0.144 1009 Planarity : 0.004 0.065 1072 Dihedral : 4.226 16.589 908 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.29 % Favored : 94.35 % Rotamer: Outliers : 4.72 % Allowed : 27.40 % Favored : 67.88 % 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: 0.48 (0.29), residues: 365 sheet: 0.28 (0.38), residues: 196 loop : -1.65 (0.38), residues: 289 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 0.036 0.002 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 127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.635 Fit side-chains REVERT: A 195 ILE cc_start: 0.7786 (mm) cc_final: 0.7452 (mm) REVERT: A 296 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6942 (mmt180) REVERT: A 393 MET cc_start: 0.0458 (ptt) cc_final: -0.0302 (mmt) REVERT: A 530 SER cc_start: 0.8322 (m) cc_final: 0.7967 (m) REVERT: A 538 MET cc_start: 0.8683 (mtp) cc_final: 0.8319 (mtp) REVERT: C 29 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8143 (mtpm) REVERT: C 85 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7913 (m) REVERT: C 123 LYS cc_start: 0.8093 (tttp) cc_final: 0.7616 (tmtt) REVERT: C 125 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6857 (pt0) REVERT: C 127 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7757 (ttmt) outliers start: 26 outliers final: 18 residues processed: 116 average time/residue: 0.9991 time to fit residues: 123.2304 Evaluate side-chains 119 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 215 SER 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 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 85 SER Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 84 GLN 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 61 optimal weight: 50.0000 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 48 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120809 restraints weight = 6704.742| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.80 r_work: 0.3157 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3714 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= 0.234 Angle : 0.595 12.018 8459 Z= 0.296 Chirality : 0.042 0.143 1009 Planarity : 0.004 0.065 1072 Dihedral : 4.293 18.307 908 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.06 % Favored : 94.71 % Rotamer: Outliers : 4.54 % Allowed : 27.77 % Favored : 67.70 % 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: -0.46 (0.30), residues: 850 helix: 0.46 (0.28), residues: 365 sheet: 0.32 (0.38), residues: 196 loop : -1.66 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.002 0.001 HIS D 54 PHE 0.012 0.001 PHE A 49 TYR 0.037 0.002 TYR A 133 ARG 0.009 0.001 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.93 seconds wall clock time: 48 minutes 30.44 seconds (2910.44 seconds total)