Starting phenix.real_space_refine on Fri Aug 22 19:23:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umx_42387/08_2025/8umx_42387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umx_42387/08_2025/8umx_42387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8umx_42387/08_2025/8umx_42387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umx_42387/08_2025/8umx_42387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8umx_42387/08_2025/8umx_42387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umx_42387/08_2025/8umx_42387.map" } resolution = 4.0 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= 0.007 sd= 0.074 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4505 2.51 5 N 1282 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7166 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2566 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "C" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2325 Classifications: {'peptide': 287} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 265} Chain: "D" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "E" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 609 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "F" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Time building chain proxies: 1.40, per 1000 atoms: 0.20 Number of scatterers: 7166 At special positions: 0 Unit cell: (94.848, 94.848, 173.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1352 8.00 N 1282 7.00 C 4505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.44 Conformation dependent library (CDL) restraints added in 381.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 52.2% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 517 through 543 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.982A pdb=" N VAL A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 removed outlier: 3.613A pdb=" N THR B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.684A pdb=" N HIS B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.765A pdb=" N ALA B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 66 removed outlier: 3.706A pdb=" N GLN B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 85 removed outlier: 3.926A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 111 Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.968A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.627A pdb=" N LEU B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 168 through 187 removed outlier: 3.506A pdb=" N LEU B 175 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 207 through 222 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.669A pdb=" N LYS B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 297 through 318 Processing helix chain 'C' and resid 51 through 74 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 147 through 173 removed outlier: 3.611A pdb=" N LEU C 160 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.547A pdb=" N PHE C 188 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 removed outlier: 3.571A pdb=" N GLU C 225 " --> pdb=" O SER C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 240 through 254 removed outlier: 3.816A pdb=" N GLN C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL C 251 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'F' and resid 75 through 80 removed outlier: 3.937A pdb=" N ARG F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 136 removed outlier: 3.628A pdb=" N MET F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 81 Processing sheet with id=AA2, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.759A pdb=" N CYS C 218 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU C 102 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER C 182 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 104 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 258 through 259 removed outlier: 3.784A pdb=" N LEU C 259 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N MET D 73 " --> pdb=" O LEU C 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 262 through 264 removed outlier: 3.801A pdb=" N ILE C 293 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL C 296 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR C 303 " --> pdb=" O GLU C 318 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR C 313 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.744A pdb=" N ILE C 268 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU D 97 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN D 108 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE D 99 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR D 118 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 86 through 88 removed outlier: 6.752A pdb=" N GLN F 108 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE F 125 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE F 106 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE F 99 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN F 108 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU F 97 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR E 74 " --> pdb=" O PRO F 61 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS F 63 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG E 72 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR F 65 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG E 70 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU F 67 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU E 68 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY F 69 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 66 " --> pdb=" O GLY F 69 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU E 64 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET F 73 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP E 98 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 99 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ILE E 106 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE E 125 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN E 108 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR E 118 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 87 " --> pdb=" O VAL E 120 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1134 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: 0.84 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2489 1.34 - 1.46: 1318 1.46 - 1.58: 3393 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7253 Sorted by residual: bond pdb=" CB ASP E 59 " pdb=" CG ASP E 59 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" CG LEU E 97 " pdb=" CD1 LEU E 97 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB ASP E 116 " pdb=" CG ASP E 116 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CB ASP F 90 " pdb=" CG ASP F 90 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CB LYS C 108 " pdb=" CG LYS C 108 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 ... (remaining 7248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 9549 1.97 - 3.95: 207 3.95 - 5.92: 36 5.92 - 7.90: 12 7.90 - 9.87: 9 Bond angle restraints: 9813 Sorted by residual: angle pdb=" N ASP D 116 " pdb=" CA ASP D 116 " pdb=" CB ASP D 116 " ideal model delta sigma weight residual 114.17 109.01 5.16 1.14e+00 7.69e-01 2.05e+01 angle pdb=" CA LYS C 170 " pdb=" CB LYS C 170 " pdb=" CG LYS C 170 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CA LYS C 108 " pdb=" CB LYS C 108 " pdb=" CG LYS C 108 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CA GLU A 538 " pdb=" CB GLU A 538 " pdb=" CG GLU A 538 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA MET D 73 " pdb=" CB MET D 73 " pdb=" CG MET D 73 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 ... (remaining 9808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 3849 17.76 - 35.52: 504 35.52 - 53.29: 124 53.29 - 71.05: 27 71.05 - 88.81: 8 Dihedral angle restraints: 4512 sinusoidal: 1892 harmonic: 2620 Sorted by residual: dihedral pdb=" CA ARG C 44 " pdb=" C ARG C 44 " pdb=" N ARG C 45 " pdb=" CA ARG C 45 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP E 59 " pdb=" C ASP E 59 " pdb=" N ILE E 60 " pdb=" CA ILE E 60 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA THR E 127 " pdb=" C THR E 127 " pdb=" N PRO E 128 " pdb=" CA PRO E 128 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 892 0.047 - 0.095: 221 0.095 - 0.142: 51 0.142 - 0.189: 6 0.189 - 0.237: 1 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CB ILE F 60 " pdb=" CA ILE F 60 " pdb=" CG1 ILE F 60 " pdb=" CG2 ILE F 60 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE D 125 " pdb=" N ILE D 125 " pdb=" C ILE D 125 " pdb=" CB ILE D 125 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ILE F 57 " pdb=" N ILE F 57 " pdb=" C ILE F 57 " pdb=" CB ILE F 57 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 1168 not shown) Planarity restraints: 1282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 59 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C ASP E 59 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP E 59 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE E 60 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 116 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ASP E 116 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP E 116 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS E 117 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 127 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO F 128 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 128 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 128 " 0.026 5.00e-02 4.00e+02 ... (remaining 1279 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 363 2.72 - 3.26: 7841 3.26 - 3.81: 12254 3.81 - 4.35: 13715 4.35 - 4.90: 22407 Nonbonded interactions: 56580 Sorted by model distance: nonbonded pdb=" O GLY B 194 " pdb=" OG1 THR B 198 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR D 74 " pdb=" OE1 GLU D 77 " model vdw 2.185 3.040 nonbonded pdb=" N GLU E 77 " pdb=" OE1 GLU E 77 " model vdw 2.200 3.120 nonbonded pdb=" ND2 ASN D 102 " pdb=" O PRO E 61 " model vdw 2.200 3.120 nonbonded pdb=" OG1 THR F 127 " pdb=" OE1 GLU F 130 " model vdw 2.201 3.040 ... (remaining 56575 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 Found NCS groups: ncs_group { reference = (chain 'D' and resid 56 through 134) selection = chain 'E' selection = (chain 'F' and resid 56 through 134) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.860 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.320 Find NCS groups from input model: 0.060 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.003 0.039 7253 Z= 0.143 Angle : 0.771 9.869 9813 Z= 0.391 Chirality : 0.045 0.237 1171 Planarity : 0.004 0.049 1282 Dihedral : 17.117 88.811 2806 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 0.50 % Allowed : 28.81 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -0.01 (0.30), residues: 894 helix: 1.15 (0.26), residues: 426 sheet: -1.56 (0.53), residues: 95 loop : -0.88 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 94 TYR 0.006 0.001 TYR C 165 PHE 0.027 0.002 PHE B 234 TRP 0.008 0.001 TRP C 246 HIS 0.002 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7253) covalent geometry : angle 0.77081 ( 9813) hydrogen bonds : bond 0.14522 ( 396) hydrogen bonds : angle 6.52299 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5575 (tpt) cc_final: 0.4092 (tpt) REVERT: B 321 MET cc_start: 0.7563 (mmt) cc_final: 0.7178 (mmt) REVERT: C 223 MET cc_start: 0.9229 (mmm) cc_final: 0.8968 (mmm) REVERT: C 288 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8044 (mmtt) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0729 time to fit residues: 5.1754 Evaluate side-chains 44 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain F residue 60 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.035309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.026107 restraints weight = 98730.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.026565 restraints weight = 68558.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.026868 restraints weight = 53113.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.027094 restraints weight = 44399.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.027265 restraints weight = 39113.977| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7253 Z= 0.126 Angle : 0.666 8.225 9813 Z= 0.339 Chirality : 0.043 0.238 1171 Planarity : 0.005 0.045 1282 Dihedral : 4.701 45.272 1003 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 4.15 % Allowed : 23.52 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.07 (0.29), residues: 894 helix: 1.18 (0.25), residues: 433 sheet: -1.11 (0.55), residues: 87 loop : -0.97 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 72 TYR 0.011 0.001 TYR E 104 PHE 0.016 0.001 PHE B 26 TRP 0.002 0.001 TRP A 554 HIS 0.008 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7253) covalent geometry : angle 0.66588 ( 9813) hydrogen bonds : bond 0.03473 ( 396) hydrogen bonds : angle 5.10488 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 47 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7976 (tpt) cc_final: 0.7301 (tpt) REVERT: B 113 MET cc_start: 0.8376 (pmm) cc_final: 0.7906 (pmm) REVERT: B 158 MET cc_start: 0.8798 (ptp) cc_final: 0.8442 (ppp) REVERT: C 157 MET cc_start: 0.9283 (ptm) cc_final: 0.8989 (ptp) outliers start: 33 outliers final: 14 residues processed: 79 average time/residue: 0.0792 time to fit residues: 8.6664 Evaluate side-chains 55 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 67 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.034772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.025481 restraints weight = 102315.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.025965 restraints weight = 68856.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.026275 restraints weight = 52758.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.026485 restraints weight = 43885.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026646 restraints weight = 38967.302| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7253 Z= 0.158 Angle : 0.629 7.395 9813 Z= 0.322 Chirality : 0.042 0.193 1171 Planarity : 0.004 0.059 1282 Dihedral : 4.703 49.401 999 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 5.16 % Allowed : 22.52 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -0.02 (0.29), residues: 894 helix: 1.20 (0.25), residues: 437 sheet: -1.18 (0.52), residues: 90 loop : -1.17 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 72 TYR 0.010 0.001 TYR E 104 PHE 0.011 0.001 PHE B 26 TRP 0.005 0.001 TRP C 246 HIS 0.009 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7253) covalent geometry : angle 0.62884 ( 9813) hydrogen bonds : bond 0.03340 ( 396) hydrogen bonds : angle 4.98138 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 44 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7933 (tpt) cc_final: 0.7201 (tpt) REVERT: B 113 MET cc_start: 0.8223 (pmm) cc_final: 0.7901 (pmm) REVERT: B 158 MET cc_start: 0.8604 (ptp) cc_final: 0.8370 (ppp) REVERT: C 157 MET cc_start: 0.9190 (ptm) cc_final: 0.8975 (ptp) outliers start: 41 outliers final: 23 residues processed: 81 average time/residue: 0.0829 time to fit residues: 8.9623 Evaluate side-chains 64 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.034772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.025459 restraints weight = 99788.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025942 restraints weight = 68526.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.026252 restraints weight = 52722.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.026490 restraints weight = 44117.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.026650 restraints weight = 38722.447| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7253 Z= 0.125 Angle : 0.627 10.321 9813 Z= 0.315 Chirality : 0.043 0.222 1171 Planarity : 0.004 0.057 1282 Dihedral : 4.635 48.889 999 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 4.40 % Allowed : 22.77 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.01 (0.29), residues: 894 helix: 1.24 (0.25), residues: 439 sheet: -1.07 (0.52), residues: 90 loop : -1.21 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.009 0.001 TYR E 104 PHE 0.010 0.001 PHE B 234 TRP 0.005 0.001 TRP C 246 HIS 0.008 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7253) covalent geometry : angle 0.62689 ( 9813) hydrogen bonds : bond 0.03156 ( 396) hydrogen bonds : angle 4.88438 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 42 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8340 (tpt) cc_final: 0.7751 (tpt) REVERT: B 113 MET cc_start: 0.8696 (pmm) cc_final: 0.8385 (pmm) REVERT: B 158 MET cc_start: 0.8927 (ptp) cc_final: 0.8585 (ppp) REVERT: C 157 MET cc_start: 0.9314 (ptm) cc_final: 0.9075 (ptp) REVERT: C 223 MET cc_start: 0.9575 (mmm) cc_final: 0.8885 (mmm) outliers start: 35 outliers final: 22 residues processed: 74 average time/residue: 0.0701 time to fit residues: 7.4846 Evaluate side-chains 62 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.034914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.025684 restraints weight = 100342.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.026172 restraints weight = 68946.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.026498 restraints weight = 53012.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.026738 restraints weight = 43993.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.026909 restraints weight = 38598.793| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7253 Z= 0.115 Angle : 0.640 10.876 9813 Z= 0.315 Chirality : 0.042 0.151 1171 Planarity : 0.004 0.055 1282 Dihedral : 4.532 48.513 999 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 4.03 % Allowed : 23.77 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.10 (0.29), residues: 894 helix: 1.24 (0.25), residues: 436 sheet: -0.79 (0.58), residues: 76 loop : -1.11 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.007 0.001 TYR E 104 PHE 0.010 0.001 PHE B 234 TRP 0.004 0.001 TRP C 246 HIS 0.008 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7253) covalent geometry : angle 0.64030 ( 9813) hydrogen bonds : bond 0.03057 ( 396) hydrogen bonds : angle 4.85402 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 42 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.5749 (pp30) REVERT: B 1 MET cc_start: 0.8390 (tpt) cc_final: 0.7820 (tpt) REVERT: B 113 MET cc_start: 0.8718 (pmm) cc_final: 0.8431 (pmm) REVERT: B 134 LEU cc_start: 0.9827 (tp) cc_final: 0.9612 (mt) REVERT: B 158 MET cc_start: 0.8880 (ptp) cc_final: 0.8643 (ppp) REVERT: C 108 LYS cc_start: 0.9671 (mmtt) cc_final: 0.9347 (mmtm) REVERT: C 157 MET cc_start: 0.9294 (ptm) cc_final: 0.9061 (ptp) REVERT: C 223 MET cc_start: 0.9542 (mmm) cc_final: 0.8706 (mmm) REVERT: E 89 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8848 (pp) outliers start: 32 outliers final: 19 residues processed: 71 average time/residue: 0.0749 time to fit residues: 7.4384 Evaluate side-chains 62 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 overall best weight: 3.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.033580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.024776 restraints weight = 104252.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.025240 restraints weight = 71295.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.025547 restraints weight = 54761.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.025751 restraints weight = 45540.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025914 restraints weight = 40120.902| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7253 Z= 0.226 Angle : 0.712 10.489 9813 Z= 0.359 Chirality : 0.044 0.297 1171 Planarity : 0.004 0.055 1282 Dihedral : 4.628 50.590 999 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 4.53 % Allowed : 24.28 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -0.10 (0.29), residues: 894 helix: 1.09 (0.25), residues: 438 sheet: -1.30 (0.50), residues: 91 loop : -1.13 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 72 TYR 0.010 0.001 TYR C 313 PHE 0.011 0.002 PHE C 137 TRP 0.018 0.002 TRP C 246 HIS 0.008 0.002 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7253) covalent geometry : angle 0.71155 ( 9813) hydrogen bonds : bond 0.03396 ( 396) hydrogen bonds : angle 5.06933 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 41 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 MET cc_start: 0.8660 (ppp) cc_final: 0.8228 (tmm) REVERT: B 1 MET cc_start: 0.8118 (tpt) cc_final: 0.7423 (tpt) REVERT: B 113 MET cc_start: 0.8588 (pmm) cc_final: 0.8367 (pmm) REVERT: B 330 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8121 (t80) REVERT: C 223 MET cc_start: 0.9306 (mmm) cc_final: 0.8487 (mmm) outliers start: 36 outliers final: 26 residues processed: 75 average time/residue: 0.0680 time to fit residues: 7.0384 Evaluate side-chains 66 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 39 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.034011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.025125 restraints weight = 103671.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.025622 restraints weight = 69290.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.025948 restraints weight = 52447.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.026160 restraints weight = 43226.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.026321 restraints weight = 37958.049| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7253 Z= 0.150 Angle : 0.685 10.747 9813 Z= 0.340 Chirality : 0.043 0.257 1171 Planarity : 0.004 0.035 1282 Dihedral : 4.270 17.288 995 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 3.90 % Allowed : 25.53 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -0.03 (0.29), residues: 894 helix: 1.12 (0.25), residues: 439 sheet: -1.14 (0.50), residues: 91 loop : -1.09 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.008 0.001 TYR C 313 PHE 0.010 0.001 PHE B 236 TRP 0.009 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7253) covalent geometry : angle 0.68506 ( 9813) hydrogen bonds : bond 0.03153 ( 396) hydrogen bonds : angle 4.98011 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 39 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8519 (tpt) cc_final: 0.7962 (tpt) REVERT: B 71 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7649 (tp) REVERT: B 113 MET cc_start: 0.8760 (pmm) cc_final: 0.8555 (pmm) REVERT: C 223 MET cc_start: 0.9467 (mmm) cc_final: 0.8631 (mmm) REVERT: D 71 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8896 (m) REVERT: E 89 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8897 (pp) outliers start: 31 outliers final: 21 residues processed: 69 average time/residue: 0.0763 time to fit residues: 7.1843 Evaluate side-chains 64 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.034394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.025513 restraints weight = 101257.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.026000 restraints weight = 68202.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.026327 restraints weight = 51969.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026561 restraints weight = 42904.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.026712 restraints weight = 37445.333| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7253 Z= 0.122 Angle : 0.687 10.839 9813 Z= 0.338 Chirality : 0.044 0.335 1171 Planarity : 0.004 0.034 1282 Dihedral : 4.186 17.379 995 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 3.90 % Allowed : 25.66 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.09 (0.29), residues: 894 helix: 1.09 (0.25), residues: 438 sheet: -0.77 (0.57), residues: 76 loop : -0.94 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.008 0.001 TYR C 313 PHE 0.009 0.001 PHE B 234 TRP 0.006 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7253) covalent geometry : angle 0.68706 ( 9813) hydrogen bonds : bond 0.03082 ( 396) hydrogen bonds : angle 4.91284 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 45 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8138 (tpt) cc_final: 0.7262 (tpt) REVERT: B 330 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8007 (t80) REVERT: C 108 LYS cc_start: 0.9649 (mmtt) cc_final: 0.9245 (mmtm) REVERT: C 223 MET cc_start: 0.9408 (mmm) cc_final: 0.8622 (mmm) REVERT: D 71 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8609 (m) REVERT: D 98 ASP cc_start: 0.8914 (t0) cc_final: 0.8427 (t0) REVERT: E 81 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9305 (mt) REVERT: E 89 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8891 (pp) outliers start: 31 outliers final: 25 residues processed: 75 average time/residue: 0.0894 time to fit residues: 9.1851 Evaluate side-chains 71 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 42 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.034110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.025321 restraints weight = 102860.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.025804 restraints weight = 69369.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.026135 restraints weight = 52887.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.026335 restraints weight = 43824.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.026498 restraints weight = 38553.286| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7253 Z= 0.142 Angle : 0.715 11.296 9813 Z= 0.351 Chirality : 0.044 0.333 1171 Planarity : 0.004 0.034 1282 Dihedral : 4.219 16.784 995 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 4.03 % Allowed : 25.91 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.20 (0.29), residues: 894 helix: 1.13 (0.25), residues: 440 sheet: -0.72 (0.57), residues: 77 loop : -0.83 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.008 0.001 TYR C 313 PHE 0.009 0.001 PHE B 234 TRP 0.008 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7253) covalent geometry : angle 0.71486 ( 9813) hydrogen bonds : bond 0.03119 ( 396) hydrogen bonds : angle 4.90720 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 42 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 MET cc_start: 0.8962 (ppp) cc_final: 0.8557 (tmm) REVERT: B 1 MET cc_start: 0.8132 (tpt) cc_final: 0.7248 (tpt) REVERT: B 330 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.8118 (t80) REVERT: C 108 LYS cc_start: 0.9632 (mmtt) cc_final: 0.9238 (mmtm) REVERT: C 223 MET cc_start: 0.9424 (mmm) cc_final: 0.8664 (mmm) REVERT: D 71 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8547 (m) REVERT: D 98 ASP cc_start: 0.8913 (t0) cc_final: 0.8433 (t0) REVERT: E 81 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9328 (mt) REVERT: F 75 ILE cc_start: 0.9544 (OUTLIER) cc_final: 0.9225 (mp) outliers start: 32 outliers final: 24 residues processed: 73 average time/residue: 0.0812 time to fit residues: 8.2500 Evaluate side-chains 70 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 85 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS D 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.034624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.025821 restraints weight = 101966.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.026319 restraints weight = 68675.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.026616 restraints weight = 52285.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.026855 restraints weight = 43816.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.026989 restraints weight = 38292.630| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7253 Z= 0.118 Angle : 0.733 12.143 9813 Z= 0.352 Chirality : 0.044 0.333 1171 Planarity : 0.004 0.034 1282 Dihedral : 4.164 16.804 995 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 3.02 % Allowed : 26.92 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.24 (0.29), residues: 894 helix: 1.13 (0.25), residues: 438 sheet: -0.55 (0.58), residues: 76 loop : -0.78 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 21 TYR 0.005 0.001 TYR E 104 PHE 0.010 0.001 PHE B 234 TRP 0.004 0.001 TRP C 169 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7253) covalent geometry : angle 0.73304 ( 9813) hydrogen bonds : bond 0.03045 ( 396) hydrogen bonds : angle 4.83806 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8482 (tpt) cc_final: 0.7765 (tpt) REVERT: C 108 LYS cc_start: 0.9710 (mmtt) cc_final: 0.9464 (mmtm) REVERT: C 223 MET cc_start: 0.9572 (mmm) cc_final: 0.8855 (mmm) REVERT: D 71 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8762 (m) REVERT: D 98 ASP cc_start: 0.9015 (t0) cc_final: 0.8578 (t0) REVERT: E 81 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9363 (mt) outliers start: 24 outliers final: 20 residues processed: 67 average time/residue: 0.0704 time to fit residues: 6.6746 Evaluate side-chains 64 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 169 TRP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.034628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.025804 restraints weight = 102134.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.026275 restraints weight = 68985.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026613 restraints weight = 52720.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.026839 restraints weight = 43612.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.026988 restraints weight = 38108.148| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7253 Z= 0.122 Angle : 0.714 12.231 9813 Z= 0.347 Chirality : 0.044 0.336 1171 Planarity : 0.004 0.034 1282 Dihedral : 4.125 16.624 995 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 3.02 % Allowed : 26.79 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.31 (0.29), residues: 894 helix: 1.20 (0.25), residues: 439 sheet: -0.57 (0.58), residues: 77 loop : -0.77 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.007 0.001 TYR C 313 PHE 0.010 0.001 PHE B 234 TRP 0.006 0.001 TRP C 246 HIS 0.008 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7253) covalent geometry : angle 0.71389 ( 9813) hydrogen bonds : bond 0.02991 ( 396) hydrogen bonds : angle 4.78848 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.06 seconds wall clock time: 24 minutes 35.35 seconds (1475.35 seconds total)