Starting phenix.real_space_refine on Thu Jul 2 06:08:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8w_29857/07_2026/8g8w_29857_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8w_29857/07_2026/8g8w_29857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8w_29857/07_2026/8g8w_29857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8w_29857/07_2026/8g8w_29857.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8w_29857/07_2026/8g8w_29857_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8w_29857/07_2026/8g8w_29857_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 P 8 5.49 5 S 23 5.16 5 C 4165 2.51 5 N 1066 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6471 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2146 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2814 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 5 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 16, 'ASP:plan': 10, 'ARG:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 169 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1349 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'GLU:plan': 12, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 3, 'HIS:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 179 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'CDL': 3, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-4': 1, 'CDL:plan-1': 2, 'CDL:plan-2': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 1.56, per 1000 atoms: 0.24 Number of scatterers: 6471 At special positions: 0 Unit cell: (72.24, 92.02, 203.82, 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) S 23 16.00 P 8 15.00 O 1209 8.00 N 1066 7.00 C 4165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 98 " 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 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 327.9 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 9 sheets defined 48.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.203A pdb=" N ASP A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.549A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 88 through 105 removed outlier: 4.341A pdb=" N ASP A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 130 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.109A pdb=" N GLU A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 205 removed outlier: 3.890A pdb=" N ASN A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 242 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 270 through 298 removed outlier: 4.158A pdb=" N LYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.931A pdb=" N ASN B 34 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'B' and resid 65 through 68 removed outlier: 4.044A pdb=" N GLU B 68 " --> pdb=" O ASP B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.882A pdb=" N THR B 94 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 153 removed outlier: 3.594A pdb=" N LEU B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 185 through 195 removed outlier: 4.219A pdb=" N GLY B 189 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'B' and resid 274 through 277 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.740A pdb=" N ILE B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 407 through 418 removed outlier: 3.966A pdb=" N ASP B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 removed outlier: 3.650A pdb=" N GLU B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.518A pdb=" N LYS B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.614A pdb=" N PHE B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.515A pdb=" N TYR C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.532A pdb=" N TYR C 112 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.594A pdb=" N PHE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 408 removed outlier: 3.602A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.723A pdb=" N GLY B 13 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 37 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 52 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG B 41 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 159 removed outlier: 6.496A pdb=" N LEU B 128 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLU B 159 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE B 130 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA B 385 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 348 Processing sheet with id=AA6, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.813A pdb=" N GLY C 13 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 41 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C 50 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.813A pdb=" N GLY C 13 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 120 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 163 removed outlier: 7.536A pdb=" N ILE C 134 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C 387 " --> pdb=" O ILE C 233 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1017 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: 1.02 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1069 1.32 - 1.45: 1808 1.45 - 1.57: 3699 1.57 - 1.69: 15 1.69 - 1.82: 36 Bond restraints: 6627 Sorted by residual: bond pdb=" OB5 CDL A 403 " pdb=" PB2 CDL A 403 " ideal model delta sigma weight residual 1.657 1.604 0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" OB5 CDL A 404 " pdb=" PB2 CDL A 404 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" CB3 CDL A 403 " pdb=" OB5 CDL A 403 " ideal model delta sigma weight residual 1.403 1.453 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" CB3 CDL A 404 " pdb=" OB5 CDL A 404 " ideal model delta sigma weight residual 1.403 1.453 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" CA3 CDL A 404 " pdb=" OA5 CDL A 404 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 6622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 8937 2.52 - 5.04: 114 5.04 - 7.57: 17 7.57 - 10.09: 8 10.09 - 12.61: 3 Bond angle restraints: 9079 Sorted by residual: angle pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sigma weight residual 120.50 133.11 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C1' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " ideal model delta sigma weight residual 111.00 99.26 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 119.63 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB MET B 442 " pdb=" CG MET B 442 " pdb=" SD MET B 442 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" PB GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sigma weight residual 120.50 130.08 -9.58 3.00e+00 1.11e-01 1.02e+01 ... (remaining 9074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 3784 35.44 - 70.89: 101 70.89 - 106.33: 5 106.33 - 141.77: 1 141.77 - 177.22: 2 Dihedral angle restraints: 3893 sinusoidal: 1324 harmonic: 2569 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -78.19 -177.22 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 83.42 -152.34 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 171.36 132.44 1 2.00e+01 2.50e-03 4.02e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 935 0.070 - 0.140: 101 0.140 - 0.210: 3 0.210 - 0.280: 1 0.280 - 0.350: 3 Chirality restraints: 1043 Sorted by residual: chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.39 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB4 CDL A 403 " pdb=" CB3 CDL A 403 " pdb=" CB6 CDL A 403 " pdb=" OB6 CDL A 403 " both_signs ideal model delta sigma weight residual False -2.61 -2.29 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.78 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1040 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 89 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO C 90 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 231 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO C 232 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 232 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 232 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 454 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 455 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 455 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 455 " 0.020 5.00e-02 4.00e+02 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1151 2.77 - 3.30: 5841 3.30 - 3.83: 10176 3.83 - 4.37: 10576 4.37 - 4.90: 19789 Nonbonded interactions: 47533 Sorted by model distance: nonbonded pdb=" OG SER C 55 " pdb=" OH TYR C 112 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP B 179 " pdb=" OG SER B 391 " model vdw 2.238 3.040 nonbonded pdb=" NE2 GLN A 42 " pdb=" OD2 ASP A 234 " model vdw 2.309 3.120 nonbonded pdb=" O ASP C 75 " pdb=" N ASN C 79 " model vdw 2.316 3.120 nonbonded pdb=" NZ LYS A 138 " pdb=" O1B GTP A 401 " model vdw 2.324 3.120 ... (remaining 47528 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.960 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.004 0.053 6630 Z= 0.204 Angle : 0.701 12.609 9086 Z= 0.313 Chirality : 0.046 0.350 1043 Planarity : 0.004 0.066 1152 Dihedral : 16.385 177.216 2245 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.18 % Allowed : 19.37 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.29), residues: 880 helix: 2.73 (0.28), residues: 344 sheet: 0.79 (0.40), residues: 144 loop : -0.10 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.011 0.001 TYR C 82 PHE 0.008 0.001 PHE A 286 TRP 0.010 0.001 TRP A 281 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 ( 6627) covalent geometry : angle 0.70107 / 0.31 ( 9079) SS BOND : bond 0.00197 / 0.10 ( 2) SS BOND : angle 0.29089 / 0.12 ( 4) hydrogen bonds : bond 0.13923 / 9.53 ( 363) hydrogen bonds : angle 5.42106 / 3.91 ( 1017) link_ALPHA1-4 : bond 0.00106 / 0.06 ( 1) link_ALPHA1-4 : angle 0.83297 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.289 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.0679 time to fit residues: 5.4459 Evaluate side-chains 50 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.157441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137035 restraints weight = 10783.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137034 restraints weight = 9819.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136987 restraints weight = 9515.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137031 restraints weight = 9249.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137021 restraints weight = 9405.701| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6630 Z= 0.138 Angle : 0.531 7.895 9086 Z= 0.263 Chirality : 0.041 0.164 1043 Planarity : 0.004 0.055 1152 Dihedral : 12.403 177.770 1124 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.48 % Allowed : 18.63 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.29), residues: 880 helix: 2.68 (0.28), residues: 361 sheet: 0.83 (0.40), residues: 143 loop : -0.09 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 22 TYR 0.008 0.001 TYR B 227 PHE 0.007 0.001 PHE B 182 TRP 0.005 0.001 TRP A 281 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6627) covalent geometry : angle 0.53058 / 0.26 ( 9079) SS BOND : bond 0.00269 / 0.14 ( 2) SS BOND : angle 0.26338 / 0.12 ( 4) hydrogen bonds : bond 0.04610 / 3.11 ( 363) hydrogen bonds : angle 4.57559 / 3.29 ( 1017) link_ALPHA1-4 : bond 0.00105 / 0.06 ( 1) link_ALPHA1-4 : angle 1.29407 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.232 Fit side-chains REVERT: A 292 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8544 (tt) REVERT: B 41 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8817 (ptp-170) REVERT: B 106 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7346 (t80) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.0682 time to fit residues: 5.8538 Evaluate side-chains 53 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 106 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN B 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.152660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132577 restraints weight = 10727.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129478 restraints weight = 12763.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129911 restraints weight = 11709.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130017 restraints weight = 10748.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130018 restraints weight = 10408.996| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6630 Z= 0.197 Angle : 0.584 6.749 9086 Z= 0.294 Chirality : 0.043 0.176 1043 Planarity : 0.005 0.057 1152 Dihedral : 12.819 176.661 1124 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.06 % Allowed : 16.79 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.28), residues: 880 helix: 2.45 (0.27), residues: 358 sheet: 0.67 (0.40), residues: 143 loop : -0.24 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 22 TYR 0.012 0.001 TYR C 97 PHE 0.014 0.002 PHE A 224 TRP 0.006 0.001 TRP A 281 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 6627) covalent geometry : angle 0.58393 / 0.29 ( 9079) SS BOND : bond 0.00385 / 0.19 ( 2) SS BOND : angle 0.45113 / 0.23 ( 4) hydrogen bonds : bond 0.05553 / 3.75 ( 363) hydrogen bonds : angle 4.69121 / 3.38 ( 1017) link_ALPHA1-4 : bond 0.00307 / 0.16 ( 1) link_ALPHA1-4 : angle 1.27345 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.276 Fit side-chains REVERT: A 155 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8641 (m) REVERT: B 106 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7418 (t80) outliers start: 22 outliers final: 11 residues processed: 68 average time/residue: 0.0663 time to fit residues: 6.6131 Evaluate side-chains 62 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.153454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135851 restraints weight = 10777.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133972 restraints weight = 15014.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134376 restraints weight = 14818.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134594 restraints weight = 12214.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134593 restraints weight = 11235.452| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6630 Z= 0.167 Angle : 0.560 6.545 9086 Z= 0.279 Chirality : 0.042 0.168 1043 Planarity : 0.005 0.053 1152 Dihedral : 12.555 178.898 1124 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.77 % Allowed : 18.45 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.28), residues: 880 helix: 2.49 (0.27), residues: 358 sheet: 0.70 (0.40), residues: 139 loop : -0.24 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.010 0.001 TYR B 98 PHE 0.011 0.001 PHE A 224 TRP 0.005 0.001 TRP C 56 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 6627) covalent geometry : angle 0.55960 / 0.28 ( 9079) SS BOND : bond 0.00358 / 0.18 ( 2) SS BOND : angle 0.34302 / 0.17 ( 4) hydrogen bonds : bond 0.04936 / 3.32 ( 363) hydrogen bonds : angle 4.56725 / 3.29 ( 1017) link_ALPHA1-4 : bond 0.00370 / 0.19 ( 1) link_ALPHA1-4 : angle 1.46113 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8643 (m) REVERT: A 168 GLU cc_start: 0.7873 (tp30) cc_final: 0.7651 (tp30) REVERT: B 30 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7436 (pp) REVERT: C 10 SER cc_start: 0.6485 (m) cc_final: 0.6045 (t) outliers start: 15 outliers final: 10 residues processed: 65 average time/residue: 0.0624 time to fit residues: 5.9138 Evaluate side-chains 63 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.154697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133264 restraints weight = 10886.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132580 restraints weight = 14164.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132571 restraints weight = 12796.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132572 restraints weight = 12043.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132572 restraints weight = 12021.187| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6630 Z= 0.135 Angle : 0.530 6.609 9086 Z= 0.264 Chirality : 0.041 0.163 1043 Planarity : 0.004 0.051 1152 Dihedral : 12.182 176.423 1124 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.69 % Allowed : 18.08 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.29), residues: 880 helix: 2.61 (0.28), residues: 357 sheet: 0.67 (0.39), residues: 143 loop : -0.17 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.009 0.001 TYR B 227 PHE 0.008 0.001 PHE A 224 TRP 0.004 0.001 TRP C 56 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 6627) covalent geometry : angle 0.52980 / 0.26 ( 9079) SS BOND : bond 0.00302 / 0.15 ( 2) SS BOND : angle 0.27619 / 0.13 ( 4) hydrogen bonds : bond 0.04515 / 3.03 ( 363) hydrogen bonds : angle 4.42674 / 3.19 ( 1017) link_ALPHA1-4 : bond 0.00053 / 0.03 ( 1) link_ALPHA1-4 : angle 1.29329 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8597 (m) REVERT: A 168 GLU cc_start: 0.7817 (tp30) cc_final: 0.7595 (tp30) REVERT: B 30 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7258 (pp) REVERT: C 10 SER cc_start: 0.6533 (m) cc_final: 0.6026 (t) outliers start: 20 outliers final: 13 residues processed: 72 average time/residue: 0.0615 time to fit residues: 6.5682 Evaluate side-chains 66 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.0010 chunk 30 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142170 restraints weight = 10844.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140520 restraints weight = 17286.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140102 restraints weight = 18282.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138309 restraints weight = 21101.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138753 restraints weight = 18187.702| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6630 Z= 0.129 Angle : 0.532 6.633 9086 Z= 0.263 Chirality : 0.041 0.164 1043 Planarity : 0.004 0.049 1152 Dihedral : 11.963 176.058 1124 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.69 % Allowed : 18.08 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.29), residues: 880 helix: 2.64 (0.27), residues: 358 sheet: 0.71 (0.39), residues: 143 loop : -0.15 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.009 0.001 TYR B 227 PHE 0.007 0.001 PHE A 224 TRP 0.004 0.001 TRP C 56 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6627) covalent geometry : angle 0.53198 / 0.26 ( 9079) SS BOND : bond 0.00279 / 0.14 ( 2) SS BOND : angle 0.23505 / 0.11 ( 4) hydrogen bonds : bond 0.04335 / 2.91 ( 363) hydrogen bonds : angle 4.34670 / 3.13 ( 1017) link_ALPHA1-4 : bond 0.00098 / 0.05 ( 1) link_ALPHA1-4 : angle 1.28623 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8588 (m) REVERT: A 168 GLU cc_start: 0.7775 (tp30) cc_final: 0.7528 (tp30) REVERT: A 285 MET cc_start: 0.7902 (tmm) cc_final: 0.7442 (tmm) REVERT: B 30 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7284 (pp) REVERT: C 10 SER cc_start: 0.6372 (m) cc_final: 0.5988 (t) outliers start: 20 outliers final: 13 residues processed: 70 average time/residue: 0.0626 time to fit residues: 6.4664 Evaluate side-chains 65 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.153352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.142693 restraints weight = 10748.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138023 restraints weight = 16937.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137598 restraints weight = 21085.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137560 restraints weight = 17548.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137813 restraints weight = 15409.029| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6630 Z= 0.129 Angle : 0.528 6.632 9086 Z= 0.262 Chirality : 0.041 0.163 1043 Planarity : 0.004 0.050 1152 Dihedral : 11.847 175.540 1124 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.51 % Allowed : 18.82 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.29), residues: 880 helix: 2.68 (0.27), residues: 358 sheet: 0.73 (0.39), residues: 143 loop : -0.14 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.009 0.001 TYR B 227 PHE 0.007 0.001 PHE A 224 TRP 0.004 0.001 TRP C 56 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6627) covalent geometry : angle 0.52813 / 0.26 ( 9079) SS BOND : bond 0.00286 / 0.15 ( 2) SS BOND : angle 0.24510 / 0.12 ( 4) hydrogen bonds : bond 0.04270 / 2.87 ( 363) hydrogen bonds : angle 4.29376 / 3.09 ( 1017) link_ALPHA1-4 : bond 0.00141 / 0.07 ( 1) link_ALPHA1-4 : angle 1.28737 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7380 (tm-30) REVERT: A 155 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8613 (m) REVERT: A 168 GLU cc_start: 0.7982 (tp30) cc_final: 0.7723 (tp30) REVERT: B 30 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7308 (pp) REVERT: B 186 ASP cc_start: 0.8280 (p0) cc_final: 0.7962 (p0) REVERT: C 10 SER cc_start: 0.6410 (m) cc_final: 0.6017 (t) outliers start: 19 outliers final: 15 residues processed: 69 average time/residue: 0.0632 time to fit residues: 6.4031 Evaluate side-chains 68 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.151746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140918 restraints weight = 10768.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139005 restraints weight = 17516.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.138603 restraints weight = 17960.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137590 restraints weight = 18081.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137798 restraints weight = 16680.805| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6630 Z= 0.157 Angle : 0.560 6.601 9086 Z= 0.278 Chirality : 0.042 0.168 1043 Planarity : 0.004 0.049 1152 Dihedral : 11.840 175.835 1124 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.69 % Allowed : 19.00 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.29), residues: 880 helix: 2.62 (0.27), residues: 357 sheet: 0.69 (0.40), residues: 143 loop : -0.22 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.010 0.001 TYR B 227 PHE 0.009 0.001 PHE A 224 TRP 0.004 0.001 TRP B 39 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6627) covalent geometry : angle 0.56005 / 0.28 ( 9079) SS BOND : bond 0.00339 / 0.17 ( 2) SS BOND : angle 0.32646 / 0.16 ( 4) hydrogen bonds : bond 0.04663 / 3.14 ( 363) hydrogen bonds : angle 4.38714 / 3.16 ( 1017) link_ALPHA1-4 : bond 0.00069 / 0.04 ( 1) link_ALPHA1-4 : angle 1.28349 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.298 Fit side-chains REVERT: A 155 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8642 (m) REVERT: A 168 GLU cc_start: 0.7991 (tp30) cc_final: 0.7733 (tp30) REVERT: A 285 MET cc_start: 0.7933 (tmm) cc_final: 0.7410 (tmm) REVERT: B 30 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7404 (pp) REVERT: B 106 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7286 (t80) REVERT: C 10 SER cc_start: 0.6406 (m) cc_final: 0.6045 (t) outliers start: 20 outliers final: 13 residues processed: 69 average time/residue: 0.0673 time to fit residues: 6.8476 Evaluate side-chains 65 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.151051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142811 restraints weight = 10897.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139194 restraints weight = 15339.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137595 restraints weight = 21308.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137643 restraints weight = 20104.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137614 restraints weight = 15024.000| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6630 Z= 0.166 Angle : 0.575 7.187 9086 Z= 0.286 Chirality : 0.042 0.170 1043 Planarity : 0.005 0.052 1152 Dihedral : 11.738 175.453 1124 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.69 % Allowed : 19.74 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.29), residues: 880 helix: 2.58 (0.28), residues: 357 sheet: 0.66 (0.40), residues: 143 loop : -0.25 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.010 0.001 TYR C 97 PHE 0.009 0.001 PHE A 224 TRP 0.004 0.001 TRP C 56 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 6627) covalent geometry : angle 0.57450 / 0.29 ( 9079) SS BOND : bond 0.00350 / 0.18 ( 2) SS BOND : angle 0.35159 / 0.18 ( 4) hydrogen bonds : bond 0.04823 / 3.26 ( 363) hydrogen bonds : angle 4.43967 / 3.20 ( 1017) link_ALPHA1-4 : bond 0.00049 / 0.03 ( 1) link_ALPHA1-4 : angle 1.38282 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.300 Fit side-chains REVERT: A 168 GLU cc_start: 0.8057 (tp30) cc_final: 0.7815 (tp30) REVERT: A 285 MET cc_start: 0.7902 (tmm) cc_final: 0.7371 (tmm) REVERT: B 30 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7407 (pp) REVERT: B 106 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7365 (t80) REVERT: C 10 SER cc_start: 0.6367 (m) cc_final: 0.6046 (t) outliers start: 20 outliers final: 15 residues processed: 68 average time/residue: 0.0677 time to fit residues: 6.7645 Evaluate side-chains 66 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139489 restraints weight = 10765.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 87)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136326 restraints weight = 18074.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136287 restraints weight = 21050.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135785 restraints weight = 19536.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136062 restraints weight = 16439.074| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6630 Z= 0.179 Angle : 0.596 8.647 9086 Z= 0.299 Chirality : 0.042 0.172 1043 Planarity : 0.005 0.050 1152 Dihedral : 11.612 175.308 1124 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.32 % Allowed : 20.30 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.29), residues: 880 helix: 2.56 (0.28), residues: 356 sheet: 0.59 (0.40), residues: 143 loop : -0.35 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.011 0.001 TYR C 97 PHE 0.012 0.001 PHE C 70 TRP 0.007 0.001 TRP B 351 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 6627) covalent geometry : angle 0.59598 / 0.30 ( 9079) SS BOND : bond 0.00369 / 0.19 ( 2) SS BOND : angle 0.39221 / 0.20 ( 4) hydrogen bonds : bond 0.04996 / 3.38 ( 363) hydrogen bonds : angle 4.50933 / 3.25 ( 1017) link_ALPHA1-4 : bond 0.00056 / 0.03 ( 1) link_ALPHA1-4 : angle 1.46608 / 0.67 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.256 Fit side-chains REVERT: A 168 GLU cc_start: 0.8132 (tp30) cc_final: 0.7892 (tp30) REVERT: A 285 MET cc_start: 0.7905 (tmm) cc_final: 0.7377 (tmm) REVERT: B 30 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7413 (pp) REVERT: B 106 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7378 (t80) REVERT: C 10 SER cc_start: 0.6368 (m) cc_final: 0.6061 (t) outliers start: 18 outliers final: 15 residues processed: 64 average time/residue: 0.0598 time to fit residues: 5.8006 Evaluate side-chains 66 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 17 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142152 restraints weight = 10827.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 91)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137899 restraints weight = 17553.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137598 restraints weight = 18606.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137702 restraints weight = 15627.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137740 restraints weight = 13863.060| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6630 Z= 0.123 Angle : 0.557 9.856 9086 Z= 0.277 Chirality : 0.041 0.160 1043 Planarity : 0.004 0.049 1152 Dihedral : 11.318 173.926 1124 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.40 % Allowed : 21.40 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.29), residues: 880 helix: 2.64 (0.28), residues: 359 sheet: 0.66 (0.39), residues: 143 loop : -0.23 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 22 TYR 0.008 0.001 TYR B 227 PHE 0.006 0.001 PHE C 40 TRP 0.005 0.001 TRP A 281 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6627) covalent geometry : angle 0.55706 / 0.28 ( 9079) SS BOND : bond 0.00281 / 0.14 ( 2) SS BOND : angle 0.22702 / 0.10 ( 4) hydrogen bonds : bond 0.04187 / 2.83 ( 363) hydrogen bonds : angle 4.31558 / 3.11 ( 1017) link_ALPHA1-4 : bond 0.00026 / 0.01 ( 1) link_ALPHA1-4 : angle 1.17024 / 0.51 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1354.75 seconds wall clock time: 24 minutes 6.10 seconds (1446.10 seconds total)