Starting phenix.real_space_refine on Thu Jul 2 08:38:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sp6_25366/07_2026/7sp6_25366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sp6_25366/07_2026/7sp6_25366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sp6_25366/07_2026/7sp6_25366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sp6_25366/07_2026/7sp6_25366.map" model { file = "/net/cci-nas-00/data/ceres_data/7sp6_25366/07_2026/7sp6_25366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sp6_25366/07_2026/7sp6_25366.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sp6_25366/07_2026/7sp6_25366.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sp6_25366/07_2026/7sp6_25366.cif" } resolution = 3.1 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1808 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 1 5.49 5 S 35 5.16 5 C 3858 2.51 5 N 977 2.21 5 O 1085 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: 5957 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4013 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 13, 'TRANS': 479} Chain breaks: 1 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' MN': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.97, per 1000 atoms: 0.16 Number of scatterers: 5957 At special positions: 0 Unit cell: (72.36, 76.68, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 35 16.00 P 1 15.00 O 1085 8.00 N 977 7.00 C 3858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 284.3 milliseconds 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 46.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.646A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.946A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.539A pdb=" N ILE A 160 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.594A pdb=" N SER A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.683A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.938A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 5.236A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix removed outlier: 3.621A pdb=" N GLN A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.967A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 360 removed outlier: 4.485A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 392 removed outlier: 3.757A pdb=" N ILE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.808A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.878A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.590A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.566A pdb=" N LYS A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.704A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 removed outlier: 8.089A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 227 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.387A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.974A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR B 68 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 7.457A pdb=" N THR B 121 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.825A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.767A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 7 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 81 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 59 removed outlier: 4.336A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 33 " --> pdb=" O ARG C 98 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1024 1.33 - 1.45: 1741 1.45 - 1.57: 3268 1.57 - 1.69: 18 1.69 - 1.82: 53 Bond restraints: 6104 Sorted by residual: bond pdb=" CBD Y01 A 601 " pdb=" CBG Y01 A 601 " ideal model delta sigma weight residual 1.520 1.643 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" CAV Y01 A 601 " pdb=" CAZ Y01 A 601 " ideal model delta sigma weight residual 1.507 1.609 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CAV Y01 A 601 " pdb=" CBC Y01 A 601 " ideal model delta sigma weight residual 1.523 1.613 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CBF Y01 A 601 " pdb=" CBH Y01 A 601 " ideal model delta sigma weight residual 1.550 1.639 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 6099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 8207 2.63 - 5.25: 46 5.25 - 7.88: 16 7.88 - 10.51: 2 10.51 - 13.14: 3 Bond angle restraints: 8274 Sorted by residual: angle pdb=" CAM Y01 A 601 " pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 111.19 124.33 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAI Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CAV Y01 A 601 " ideal model delta sigma weight residual 120.03 131.73 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CAZ Y01 A 601 " pdb=" CAV Y01 A 601 " pdb=" CBC Y01 A 601 " ideal model delta sigma weight residual 111.19 122.29 -11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C ASN A 253 " pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 122.97 120.27 2.70 9.80e-01 1.04e+00 7.60e+00 angle pdb=" CAV Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CBH Y01 A 601 " ideal model delta sigma weight residual 116.96 108.83 8.13 3.00e+00 1.11e-01 7.34e+00 ... (remaining 8269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3210 17.95 - 35.89: 258 35.89 - 53.84: 56 53.84 - 71.78: 13 71.78 - 89.73: 7 Dihedral angle restraints: 3544 sinusoidal: 1409 harmonic: 2135 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.78 37.22 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -87.74 57.74 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP A 121 " pdb=" CB ASP A 121 " pdb=" CG ASP A 121 " pdb=" OD1 ASP A 121 " ideal model delta sinusoidal sigma weight residual -30.00 -83.41 53.41 1 2.00e+01 2.50e-03 9.69e+00 ... (remaining 3541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 837 0.080 - 0.159: 56 0.159 - 0.239: 1 0.239 - 0.318: 1 0.318 - 0.398: 3 Chirality restraints: 898 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CBE Y01 A 601 " pdb=" CAP Y01 A 601 " pdb=" CBB Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.57 2.93 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CBI Y01 A 601 " pdb=" CAU Y01 A 601 " pdb=" CBE Y01 A 601 " pdb=" CBG Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 895 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 320 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 144 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.25e-01 pdb=" N PRO A 145 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 76 " 0.004 2.00e-02 2.50e+03 7.24e-03 5.24e-01 pdb=" C ASN C 76 " -0.013 2.00e-02 2.50e+03 pdb=" O ASN C 76 " 0.005 2.00e-02 2.50e+03 pdb=" N THR C 77 " 0.004 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1826 2.83 - 3.34: 5483 3.34 - 3.86: 9524 3.86 - 4.38: 10524 4.38 - 4.90: 18554 Nonbonded interactions: 45911 Sorted by model distance: nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.308 3.040 nonbonded pdb=" O TYR A 499 " pdb=" OH TYR A 507 " model vdw 2.355 3.040 nonbonded pdb=" OG SER C 51 " pdb=" O GLY C 56 " model vdw 2.358 3.040 nonbonded pdb=" ND2 ASN A 139 " pdb=" O LYS A 166 " model vdw 2.377 3.120 nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 183 " model vdw 2.379 3.040 ... (remaining 45906 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 5.120 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 0.123 6106 Z= 0.221 Angle : 0.577 13.136 8278 Z= 0.253 Chirality : 0.045 0.398 898 Planarity : 0.002 0.031 1020 Dihedral : 14.276 89.727 2180 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 1.72 (0.31), residues: 723 helix: 2.49 (0.30), residues: 302 sheet: 1.88 (0.45), residues: 135 loop : -0.78 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 66 TYR 0.011 0.001 TYR A 480 PHE 0.005 0.001 PHE C 37 TRP 0.004 0.000 TRP C 53 HIS 0.000 0.000 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 ( 6104) covalent geometry : angle 0.57670 / 0.25 ( 8274) SS BOND : bond 0.00152 / 0.07 ( 2) SS BOND : angle 0.25741 / 0.11 ( 4) hydrogen bonds : bond 0.18098 / 12.75 ( 287) hydrogen bonds : angle 5.69737 / 4.19 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.132 Fit side-chains REVERT: B 55 GLU cc_start: 0.8646 (mp0) cc_final: 0.8338 (mp0) REVERT: B 88 GLU cc_start: 0.7635 (pp20) cc_final: 0.7424 (mp0) REVERT: C 3 GLN cc_start: 0.8374 (mp-120) cc_final: 0.8172 (mm-40) REVERT: C 85 LEU cc_start: 0.8997 (mp) cc_final: 0.8758 (mp) REVERT: C 103 SER cc_start: 0.7719 (t) cc_final: 0.6861 (t) REVERT: C 118 GLN cc_start: 0.7835 (tp40) cc_final: 0.7564 (mm-40) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0477 time to fit residues: 7.8789 Evaluate side-chains 96 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.130673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112209 restraints weight = 10034.604| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.81 r_work: 0.3386 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6106 Z= 0.123 Angle : 0.503 5.263 8278 Z= 0.263 Chirality : 0.040 0.154 898 Planarity : 0.003 0.026 1020 Dihedral : 5.479 57.988 869 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.64 % Allowed : 9.13 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.43 (0.31), residues: 723 helix: 2.46 (0.29), residues: 312 sheet: 1.44 (0.44), residues: 132 loop : -1.13 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.020 0.001 TYR A 46 PHE 0.016 0.001 PHE A 185 TRP 0.009 0.001 TRP C 53 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 6104) covalent geometry : angle 0.50287 / 0.26 ( 8274) SS BOND : bond 0.00377 / 0.18 ( 2) SS BOND : angle 0.55178 / 0.26 ( 4) hydrogen bonds : bond 0.03488 / 2.34 ( 287) hydrogen bonds : angle 3.99975 / 2.79 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.139 Fit side-chains REVERT: A 426 TYR cc_start: 0.6848 (m-10) cc_final: 0.6566 (m-10) REVERT: B 3 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7561 (mm-40) REVERT: B 55 GLU cc_start: 0.9021 (mp0) cc_final: 0.8636 (mp0) REVERT: C 3 GLN cc_start: 0.8447 (mp-120) cc_final: 0.8195 (mm-40) REVERT: C 115 TYR cc_start: 0.8089 (m-10) cc_final: 0.7822 (m-10) REVERT: C 118 GLN cc_start: 0.8228 (tp40) cc_final: 0.7891 (mm-40) outliers start: 4 outliers final: 2 residues processed: 115 average time/residue: 0.0462 time to fit residues: 7.6018 Evaluate side-chains 93 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.123171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105367 restraints weight = 9985.375| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.69 r_work: 0.3296 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6106 Z= 0.114 Angle : 0.479 5.354 8278 Z= 0.251 Chirality : 0.040 0.160 898 Planarity : 0.003 0.025 1020 Dihedral : 5.281 54.547 869 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.08 % Allowed : 13.94 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.31), residues: 723 helix: 2.44 (0.29), residues: 312 sheet: 1.17 (0.42), residues: 134 loop : -1.12 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 75 TYR 0.018 0.001 TYR A 550 PHE 0.014 0.001 PHE A 185 TRP 0.007 0.001 TRP A 246 HIS 0.002 0.001 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6104) covalent geometry : angle 0.47918 / 0.25 ( 8274) SS BOND : bond 0.00264 / 0.13 ( 2) SS BOND : angle 0.28451 / 0.11 ( 4) hydrogen bonds : bond 0.03593 / 2.39 ( 287) hydrogen bonds : angle 3.64749 / 2.60 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.153 Fit side-chains REVERT: A 242 MET cc_start: 0.7822 (ttt) cc_final: 0.7617 (ttt) REVERT: A 426 TYR cc_start: 0.7444 (m-10) cc_final: 0.7059 (m-10) REVERT: B 3 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8126 (mm110) REVERT: B 55 GLU cc_start: 0.8996 (mp0) cc_final: 0.8581 (mp0) REVERT: C 2 VAL cc_start: 0.7409 (t) cc_final: 0.7167 (t) REVERT: C 3 GLN cc_start: 0.8562 (mp-120) cc_final: 0.8245 (mm-40) REVERT: C 118 GLN cc_start: 0.8131 (tp40) cc_final: 0.7830 (mm-40) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 0.0672 time to fit residues: 9.8366 Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.119624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101658 restraints weight = 10016.077| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.69 r_work: 0.3237 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6106 Z= 0.118 Angle : 0.476 5.942 8278 Z= 0.254 Chirality : 0.040 0.159 898 Planarity : 0.003 0.027 1020 Dihedral : 5.293 49.692 869 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.40 % Allowed : 15.06 % Favored : 82.53 % 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: 1.29 (0.31), residues: 723 helix: 2.41 (0.29), residues: 312 sheet: 1.07 (0.42), residues: 140 loop : -1.21 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.013 0.001 TYR A 366 PHE 0.009 0.001 PHE C 37 TRP 0.008 0.001 TRP C 53 HIS 0.001 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6104) covalent geometry : angle 0.47563 / 0.25 ( 8274) SS BOND : bond 0.00326 / 0.16 ( 2) SS BOND : angle 0.41822 / 0.16 ( 4) hydrogen bonds : bond 0.03412 / 2.25 ( 287) hydrogen bonds : angle 3.59891 / 2.54 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.262 Fit side-chains REVERT: A 426 TYR cc_start: 0.7722 (m-10) cc_final: 0.7394 (m-10) REVERT: B 3 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8158 (mm110) REVERT: B 18 LEU cc_start: 0.8097 (mp) cc_final: 0.7856 (tt) REVERT: B 55 GLU cc_start: 0.9021 (mp0) cc_final: 0.8599 (mp0) REVERT: C 2 VAL cc_start: 0.7538 (t) cc_final: 0.7291 (t) REVERT: C 3 GLN cc_start: 0.8531 (mp-120) cc_final: 0.8197 (mm-40) outliers start: 15 outliers final: 9 residues processed: 110 average time/residue: 0.0745 time to fit residues: 11.1702 Evaluate side-chains 101 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 0.0010 chunk 57 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.116932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099126 restraints weight = 10131.889| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.69 r_work: 0.3196 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6106 Z= 0.120 Angle : 0.483 6.753 8278 Z= 0.257 Chirality : 0.040 0.170 898 Planarity : 0.003 0.031 1020 Dihedral : 5.270 43.841 869 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.72 % Allowed : 16.03 % Favored : 81.25 % 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: 1.22 (0.31), residues: 723 helix: 2.39 (0.29), residues: 312 sheet: 0.94 (0.42), residues: 140 loop : -1.22 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.016 0.001 TYR C 105 PHE 0.009 0.001 PHE A 520 TRP 0.008 0.001 TRP A 246 HIS 0.001 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6104) covalent geometry : angle 0.48325 / 0.26 ( 8274) SS BOND : bond 0.00340 / 0.16 ( 2) SS BOND : angle 0.45221 / 0.18 ( 4) hydrogen bonds : bond 0.03522 / 2.31 ( 287) hydrogen bonds : angle 3.56348 / 2.54 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.233 Fit side-chains REVERT: A 242 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7612 (ttt) REVERT: A 426 TYR cc_start: 0.8007 (m-10) cc_final: 0.7683 (m-10) REVERT: B 30 LYS cc_start: 0.8298 (pttm) cc_final: 0.8038 (ptmt) REVERT: B 55 GLU cc_start: 0.9028 (mp0) cc_final: 0.8593 (mp0) REVERT: C 2 VAL cc_start: 0.7483 (t) cc_final: 0.7188 (t) REVERT: C 3 GLN cc_start: 0.8478 (mp-120) cc_final: 0.8101 (mm-40) outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 0.0850 time to fit residues: 12.0862 Evaluate side-chains 107 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097714 restraints weight = 10072.797| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.67 r_work: 0.3167 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6106 Z= 0.121 Angle : 0.494 7.916 8278 Z= 0.264 Chirality : 0.040 0.184 898 Planarity : 0.003 0.038 1020 Dihedral : 5.232 43.485 869 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.37 % Allowed : 15.87 % Favored : 80.77 % 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: 1.13 (0.31), residues: 723 helix: 2.39 (0.29), residues: 312 sheet: 0.81 (0.42), residues: 140 loop : -1.33 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 27 TYR 0.012 0.001 TYR A 550 PHE 0.011 0.001 PHE A 185 TRP 0.012 0.001 TRP A 472 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6104) covalent geometry : angle 0.49444 / 0.26 ( 8274) SS BOND : bond 0.00346 / 0.17 ( 2) SS BOND : angle 0.39290 / 0.15 ( 4) hydrogen bonds : bond 0.03522 / 2.32 ( 287) hydrogen bonds : angle 3.59724 / 2.57 ( 822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.232 Fit side-chains REVERT: A 426 TYR cc_start: 0.8180 (m-10) cc_final: 0.7893 (m-10) REVERT: B 30 LYS cc_start: 0.8397 (pttm) cc_final: 0.8119 (ptmt) REVERT: B 55 GLU cc_start: 0.9026 (mp0) cc_final: 0.8580 (mp0) REVERT: B 72 ASP cc_start: 0.8229 (p0) cc_final: 0.7997 (p0) REVERT: B 75 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8629 (pttm) REVERT: C 3 GLN cc_start: 0.8444 (mp-120) cc_final: 0.8010 (mm-40) outliers start: 21 outliers final: 15 residues processed: 108 average time/residue: 0.0814 time to fit residues: 11.7424 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.114785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097085 restraints weight = 10112.763| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.69 r_work: 0.3158 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6106 Z= 0.119 Angle : 0.494 7.799 8278 Z= 0.263 Chirality : 0.041 0.236 898 Planarity : 0.003 0.040 1020 Dihedral : 5.159 44.540 869 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.37 % Allowed : 16.03 % Favored : 80.61 % 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: 1.10 (0.31), residues: 723 helix: 2.40 (0.29), residues: 312 sheet: 0.73 (0.42), residues: 140 loop : -1.34 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.019 0.001 TYR C 105 PHE 0.009 0.001 PHE A 520 TRP 0.007 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6104) covalent geometry : angle 0.49440 / 0.26 ( 8274) SS BOND : bond 0.00403 / 0.19 ( 2) SS BOND : angle 0.52210 / 0.21 ( 4) hydrogen bonds : bond 0.03574 / 2.33 ( 287) hydrogen bonds : angle 3.60333 / 2.58 ( 822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.223 Fit side-chains REVERT: B 30 LYS cc_start: 0.8471 (pttm) cc_final: 0.8188 (ptmt) REVERT: B 55 GLU cc_start: 0.9022 (mp0) cc_final: 0.8658 (mp0) REVERT: C 3 GLN cc_start: 0.8427 (mp-120) cc_final: 0.7968 (mm-40) outliers start: 21 outliers final: 14 residues processed: 110 average time/residue: 0.0816 time to fit residues: 11.8581 Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090973 restraints weight = 10224.833| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.66 r_work: 0.3070 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6106 Z= 0.207 Angle : 0.594 8.613 8278 Z= 0.321 Chirality : 0.044 0.205 898 Planarity : 0.003 0.032 1020 Dihedral : 5.700 49.730 869 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.53 % Allowed : 16.35 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.31), residues: 723 helix: 2.21 (0.29), residues: 312 sheet: 0.64 (0.43), residues: 141 loop : -1.48 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 27 TYR 0.013 0.002 TYR A 538 PHE 0.014 0.002 PHE C 47 TRP 0.012 0.001 TRP A 71 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 6104) covalent geometry : angle 0.59407 / 0.32 ( 8274) SS BOND : bond 0.00543 / 0.26 ( 2) SS BOND : angle 0.58237 / 0.24 ( 4) hydrogen bonds : bond 0.04420 / 2.91 ( 287) hydrogen bonds : angle 3.82400 / 2.74 ( 822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.236 Fit side-chains REVERT: B 30 LYS cc_start: 0.8679 (pttm) cc_final: 0.8371 (ptmm) REVERT: B 55 GLU cc_start: 0.9018 (mp0) cc_final: 0.8668 (mp0) REVERT: B 75 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8618 (pttm) REVERT: C 3 GLN cc_start: 0.8350 (mp-120) cc_final: 0.7797 (mm-40) outliers start: 22 outliers final: 19 residues processed: 109 average time/residue: 0.0700 time to fit residues: 10.3461 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.112122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094572 restraints weight = 10064.242| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.63 r_work: 0.3129 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6106 Z= 0.115 Angle : 0.526 8.675 8278 Z= 0.280 Chirality : 0.041 0.188 898 Planarity : 0.003 0.030 1020 Dihedral : 5.423 47.737 869 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 18.43 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.30), residues: 723 helix: 2.27 (0.28), residues: 312 sheet: 0.52 (0.40), residues: 149 loop : -1.57 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.020 0.001 TYR C 105 PHE 0.010 0.001 PHE A 520 TRP 0.008 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 6104) covalent geometry : angle 0.52600 / 0.28 ( 8274) SS BOND : bond 0.00379 / 0.18 ( 2) SS BOND : angle 0.66606 / 0.27 ( 4) hydrogen bonds : bond 0.03653 / 2.39 ( 287) hydrogen bonds : angle 3.67531 / 2.64 ( 822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.251 Fit side-chains REVERT: A 333 MET cc_start: 0.8205 (mmm) cc_final: 0.7447 (mmm) REVERT: B 30 LYS cc_start: 0.8645 (pttm) cc_final: 0.8352 (ptmm) REVERT: B 55 GLU cc_start: 0.9005 (mp0) cc_final: 0.8557 (mp0) REVERT: B 75 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8632 (pttm) REVERT: C 3 GLN cc_start: 0.8401 (mp-120) cc_final: 0.7829 (mm110) outliers start: 16 outliers final: 14 residues processed: 108 average time/residue: 0.0834 time to fit residues: 12.0084 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093066 restraints weight = 10186.236| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.65 r_work: 0.3102 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6106 Z= 0.139 Angle : 0.538 9.061 8278 Z= 0.287 Chirality : 0.042 0.189 898 Planarity : 0.003 0.031 1020 Dihedral : 5.432 48.686 869 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.88 % Allowed : 18.27 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 723 helix: 2.28 (0.28), residues: 312 sheet: 0.45 (0.42), residues: 140 loop : -1.55 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 27 TYR 0.012 0.001 TYR A 414 PHE 0.011 0.001 PHE C 47 TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6104) covalent geometry : angle 0.53841 / 0.29 ( 8274) SS BOND : bond 0.00406 / 0.20 ( 2) SS BOND : angle 0.65923 / 0.27 ( 4) hydrogen bonds : bond 0.03781 / 2.48 ( 287) hydrogen bonds : angle 3.67672 / 2.64 ( 822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.239 Fit side-chains REVERT: A 481 MET cc_start: 0.8408 (mtp) cc_final: 0.8103 (mtp) REVERT: B 30 LYS cc_start: 0.8677 (pttm) cc_final: 0.8383 (ptmm) REVERT: B 55 GLU cc_start: 0.8997 (mp0) cc_final: 0.8552 (mp0) REVERT: B 75 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8647 (pttm) REVERT: C 3 GLN cc_start: 0.8411 (mp-120) cc_final: 0.7820 (mm110) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.0831 time to fit residues: 12.0658 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.0050 chunk 16 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.113805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096425 restraints weight = 10024.599| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.63 r_work: 0.3153 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6106 Z= 0.104 Angle : 0.520 8.677 8278 Z= 0.274 Chirality : 0.040 0.178 898 Planarity : 0.003 0.031 1020 Dihedral : 5.257 47.482 869 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.08 % Allowed : 19.23 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.30), residues: 723 helix: 2.41 (0.28), residues: 312 sheet: 0.46 (0.40), residues: 149 loop : -1.56 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 27 TYR 0.020 0.001 TYR C 105 PHE 0.010 0.001 PHE A 520 TRP 0.009 0.001 TRP C 53 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6104) covalent geometry : angle 0.51995 / 0.27 ( 8274) SS BOND : bond 0.00341 / 0.16 ( 2) SS BOND : angle 0.58660 / 0.23 ( 4) hydrogen bonds : bond 0.03308 / 2.14 ( 287) hydrogen bonds : angle 3.57377 / 2.57 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.03 seconds wall clock time: 24 minutes 32.53 seconds (1472.53 seconds total)