Starting phenix.real_space_refine on Wed Mar 12 04:18:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umx_42387/03_2025/8umx_42387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umx_42387/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8umx_42387/03_2025/8umx_42387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umx_42387/03_2025/8umx_42387.map" model { file = "/net/cci-nas-00/data/ceres_data/8umx_42387/03_2025/8umx_42387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umx_42387/03_2025/8umx_42387.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.57, per 1000 atoms: 0.92 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: 1.65 Conformation dependent library (CDL) restraints added in 956.8 milliseconds 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: 0.97 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: 1.97 Time building geometry restraints manager: 1.96 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: 8.830 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- 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= 0.204 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (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 TRP 0.008 0.001 TRP C 246 HIS 0.002 0.001 HIS C 295 PHE 0.027 0.002 PHE B 234 TYR 0.006 0.001 TYR C 165 ARG 0.005 0.000 ARG C 94 *********************** 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 : 0.828 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: 0.2205 time to fit residues: 15.3478 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 : 0.868 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 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 = 0.3174 r_free = 0.3174 target = 0.034990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.025829 restraints weight = 101214.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.026295 restraints weight = 70077.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.026637 restraints weight = 54197.579| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7253 Z= 0.197 Angle : 0.662 8.085 9813 Z= 0.340 Chirality : 0.043 0.200 1171 Planarity : 0.005 0.047 1282 Dihedral : 4.758 46.698 1003 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 4.78 % Allowed : 23.40 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.29), residues: 894 helix: 1.16 (0.25), residues: 434 sheet: -1.16 (0.56), residues: 81 loop : -0.98 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 554 HIS 0.007 0.001 HIS C 241 PHE 0.016 0.001 PHE B 26 TYR 0.011 0.001 TYR E 104 ARG 0.009 0.001 ARG D 72 *********************** 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 85 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 47 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7805 (tpt) cc_final: 0.7053 (tpt) REVERT: B 113 MET cc_start: 0.8231 (pmm) cc_final: 0.7585 (pmm) REVERT: B 158 MET cc_start: 0.8589 (ptp) cc_final: 0.8337 (ppp) REVERT: C 157 MET cc_start: 0.9189 (ptm) cc_final: 0.8911 (ptp) REVERT: F 67 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8411 (pt0) outliers start: 38 outliers final: 17 residues processed: 83 average time/residue: 0.1785 time to fit residues: 20.7689 Evaluate side-chains 58 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 241 HIS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 66 VAL 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 17 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 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 = 0.3155 r_free = 0.3155 target = 0.034674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.025384 restraints weight = 99652.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.025871 restraints weight = 67237.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.026202 restraints weight = 51384.658| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1756 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= 0.197 Angle : 0.620 7.753 9813 Z= 0.317 Chirality : 0.043 0.214 1171 Planarity : 0.004 0.058 1282 Dihedral : 4.727 50.541 999 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 4.78 % Allowed : 22.77 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 894 helix: 1.17 (0.25), residues: 438 sheet: -1.17 (0.52), residues: 90 loop : -1.20 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 246 HIS 0.008 0.001 HIS C 241 PHE 0.012 0.001 PHE B 234 TYR 0.011 0.001 TYR E 104 ARG 0.007 0.000 ARG D 72 *********************** 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 83 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 45 time to evaluate : 0.906 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: 0.8340 (tpt) cc_final: 0.7757 (tpt) REVERT: B 113 MET cc_start: 0.8691 (pmm) cc_final: 0.8348 (pmm) REVERT: B 158 MET cc_start: 0.8879 (ptp) cc_final: 0.8568 (ppp) REVERT: C 157 MET cc_start: 0.9330 (ptm) cc_final: 0.9090 (ptp) outliers start: 38 outliers final: 20 residues processed: 81 average time/residue: 0.1988 time to fit residues: 22.0558 Evaluate side-chains 61 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 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 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 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 0.0770 chunk 39 optimal weight: 0.3980 chunk 82 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.035064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.025681 restraints weight = 99545.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.026178 restraints weight = 67977.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.026491 restraints weight = 51887.745| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7253 Z= 0.156 Angle : 0.634 10.850 9813 Z= 0.314 Chirality : 0.043 0.215 1171 Planarity : 0.004 0.056 1282 Dihedral : 4.598 49.626 999 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 4.03 % Allowed : 23.40 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.29), residues: 894 helix: 1.22 (0.25), residues: 438 sheet: -0.65 (0.61), residues: 75 loop : -1.13 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 169 HIS 0.007 0.001 HIS C 241 PHE 0.012 0.001 PHE B 234 TYR 0.009 0.001 TYR E 104 ARG 0.005 0.000 ARG F 121 *********************** 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 74 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 42 time to evaluate : 0.920 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: 0.8163 (tpt) cc_final: 0.7534 (tpt) REVERT: B 113 MET cc_start: 0.8530 (pmm) cc_final: 0.8214 (pmm) REVERT: B 158 MET cc_start: 0.8849 (ptp) cc_final: 0.8524 (ppp) REVERT: C 108 LYS cc_start: 0.9696 (mmtt) cc_final: 0.9365 (mmtm) REVERT: C 157 MET cc_start: 0.9276 (ptm) cc_final: 0.9018 (ptp) REVERT: C 223 MET cc_start: 0.9523 (mmm) cc_final: 0.8831 (mmm) outliers start: 32 outliers final: 17 residues processed: 72 average time/residue: 0.1936 time to fit residues: 19.4237 Evaluate side-chains 58 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 241 HIS 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 E residue 64 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.0010 chunk 67 optimal weight: 9.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- 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** F 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.033583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.024765 restraints weight = 103857.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.025224 restraints weight = 70351.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.025536 restraints weight = 54054.560| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7253 Z= 0.334 Angle : 0.710 10.142 9813 Z= 0.361 Chirality : 0.043 0.160 1171 Planarity : 0.005 0.051 1282 Dihedral : 4.774 53.037 999 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.52 % Rotamer: Outliers : 4.40 % Allowed : 23.90 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 894 helix: 1.15 (0.25), residues: 437 sheet: -1.36 (0.50), residues: 91 loop : -1.18 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 246 HIS 0.007 0.002 HIS C 241 PHE 0.014 0.002 PHE B 59 TYR 0.012 0.002 TYR C 313 ARG 0.008 0.001 ARG D 72 *********************** 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 76 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 41 time to evaluate : 0.846 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: 0.8633 (tpt) cc_final: 0.8142 (tpt) REVERT: B 113 MET cc_start: 0.8839 (pmm) cc_final: 0.8594 (pmm) REVERT: C 157 MET cc_start: 0.9338 (ptm) cc_final: 0.9112 (ptp) REVERT: C 223 MET cc_start: 0.9512 (mmm) cc_final: 0.8846 (mmm) outliers start: 35 outliers final: 25 residues processed: 74 average time/residue: 0.2130 time to fit residues: 21.4203 Evaluate side-chains 62 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 132 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.034084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.025115 restraints weight = 101288.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.025592 restraints weight = 68717.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.025935 restraints weight = 52344.856| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2758 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= 0.205 Angle : 0.664 10.510 9813 Z= 0.332 Chirality : 0.043 0.231 1171 Planarity : 0.004 0.058 1282 Dihedral : 4.747 54.400 999 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 4.28 % Allowed : 24.40 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.29), residues: 894 helix: 1.20 (0.25), residues: 438 sheet: -1.11 (0.51), residues: 90 loop : -1.13 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.010 0.001 PHE B 234 TYR 0.010 0.001 TYR C 313 ARG 0.005 0.000 ARG D 72 *********************** 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 75 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 41 time to evaluate : 0.899 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 532 MET cc_start: 0.8712 (ppp) cc_final: 0.8384 (tmm) REVERT: B 1 MET cc_start: 0.8251 (tpt) cc_final: 0.7593 (tpt) REVERT: B 113 MET cc_start: 0.8587 (pmm) cc_final: 0.8372 (pmm) REVERT: B 330 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7861 (t80) REVERT: C 157 MET cc_start: 0.9237 (ptm) cc_final: 0.8987 (ptp) REVERT: C 223 MET cc_start: 0.9331 (mmm) cc_final: 0.8517 (mmm) REVERT: D 71 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8653 (m) outliers start: 34 outliers final: 24 residues processed: 73 average time/residue: 0.1912 time to fit residues: 19.4216 Evaluate side-chains 66 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 B residue 330 TYR 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 92 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 60 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.033572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.024832 restraints weight = 104458.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.025295 restraints weight = 70801.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.025597 restraints weight = 54227.219| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7253 Z= 0.265 Angle : 0.697 9.960 9813 Z= 0.353 Chirality : 0.043 0.168 1171 Planarity : 0.004 0.043 1282 Dihedral : 4.778 37.210 999 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 4.65 % Allowed : 24.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.29), residues: 894 helix: 1.03 (0.25), residues: 440 sheet: -1.22 (0.50), residues: 92 loop : -1.12 (0.36), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.012 0.002 PHE B 59 TYR 0.010 0.001 TYR C 313 ARG 0.006 0.001 ARG D 72 *********************** 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 79 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 42 time to evaluate : 0.920 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: 0.8559 (ppp) cc_final: 0.8332 (tmm) REVERT: B 1 MET cc_start: 0.8308 (tpt) cc_final: 0.7458 (tpt) REVERT: B 330 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8121 (t80) REVERT: C 58 ASN cc_start: 0.9572 (OUTLIER) cc_final: 0.9369 (t0) REVERT: C 223 MET cc_start: 0.9351 (mmm) cc_final: 0.8582 (mmm) REVERT: C 228 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8908 (ttt180) REVERT: D 71 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8838 (m) outliers start: 37 outliers final: 26 residues processed: 78 average time/residue: 0.2016 time to fit residues: 21.5365 Evaluate side-chains 68 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 38 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE 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 52 GLN Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 92 PHE 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 F residue 60 ILE 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 122 ILE Chi-restraints excluded: chain F residue 127 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** D 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.034268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.025522 restraints weight = 103536.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.026021 restraints weight = 69408.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.026345 restraints weight = 52506.918| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7253 Z= 0.167 Angle : 0.695 10.820 9813 Z= 0.343 Chirality : 0.045 0.322 1171 Planarity : 0.004 0.038 1282 Dihedral : 4.239 18.124 995 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 3.27 % Allowed : 26.92 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.29), residues: 894 helix: 1.15 (0.25), residues: 439 sheet: -0.68 (0.58), residues: 76 loop : -0.90 (0.35), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 169 HIS 0.007 0.001 HIS C 241 PHE 0.011 0.001 PHE B 234 TYR 0.007 0.001 TYR C 313 ARG 0.005 0.000 ARG C 60 *********************** 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 67 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.890 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: 0.7978 (tpt) cc_final: 0.7198 (tpt) REVERT: B 330 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8121 (t80) REVERT: C 108 LYS cc_start: 0.9640 (mmtt) cc_final: 0.9390 (mmtm) REVERT: C 223 MET cc_start: 0.9321 (mmm) cc_final: 0.8572 (mmm) REVERT: D 71 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8319 (m) REVERT: D 98 ASP cc_start: 0.8780 (t0) cc_final: 0.8301 (t0) outliers start: 26 outliers final: 18 residues processed: 67 average time/residue: 0.1668 time to fit residues: 16.2079 Evaluate side-chains 61 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 GLN 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 71 ASN Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 218 CYS 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 74 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 64 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3155 r_free = 0.3155 target = 0.034406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.025615 restraints weight = 102597.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.026111 restraints weight = 68200.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.026421 restraints weight = 51622.269| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7253 Z= 0.172 Angle : 0.692 11.190 9813 Z= 0.340 Chirality : 0.044 0.319 1171 Planarity : 0.004 0.040 1282 Dihedral : 4.207 16.929 995 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 3.14 % Allowed : 26.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 894 helix: 1.13 (0.25), residues: 439 sheet: -0.57 (0.58), residues: 76 loop : -0.82 (0.35), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.010 0.001 PHE B 234 TYR 0.006 0.001 TYR C 313 ARG 0.005 0.000 ARG E 70 *********************** 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 67 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8404 (tpt) cc_final: 0.7858 (tpt) REVERT: C 108 LYS cc_start: 0.9698 (mmtt) cc_final: 0.9438 (mmtm) REVERT: C 223 MET cc_start: 0.9587 (mmm) cc_final: 0.8820 (mmm) REVERT: D 71 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8730 (m) REVERT: D 98 ASP cc_start: 0.9037 (t0) cc_final: 0.8593 (t0) outliers start: 25 outliers final: 21 residues processed: 66 average time/residue: 0.1673 time to fit residues: 15.9937 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 : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 GLN 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 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 64 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 0.0040 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.034520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.025732 restraints weight = 104380.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.026236 restraints weight = 68793.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026487 restraints weight = 52035.685| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7253 Z= 0.179 Angle : 0.722 11.840 9813 Z= 0.352 Chirality : 0.044 0.344 1171 Planarity : 0.004 0.034 1282 Dihedral : 4.193 16.538 995 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 2.89 % Allowed : 27.17 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.29), residues: 894 helix: 1.14 (0.25), residues: 441 sheet: -0.55 (0.58), residues: 77 loop : -0.74 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.011 0.001 PHE B 234 TYR 0.015 0.001 TYR B 330 ARG 0.005 0.000 ARG E 70 ********************** 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 65 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 MET cc_start: 0.8899 (ppp) cc_final: 0.8561 (tmm) REVERT: B 1 MET cc_start: 0.8531 (tpt) cc_final: 0.8038 (tpt) REVERT: C 108 LYS cc_start: 0.9709 (mmtt) cc_final: 0.9389 (mmtm) REVERT: C 223 MET cc_start: 0.9607 (mmm) cc_final: 0.8843 (mmm) REVERT: D 71 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8774 (m) REVERT: D 98 ASP cc_start: 0.9050 (t0) cc_final: 0.8615 (t0) outliers start: 23 outliers final: 22 residues processed: 64 average time/residue: 0.1667 time to fit residues: 15.4083 Evaluate side-chains 65 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 GLN 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 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 64 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 122 ILE Chi-restraints excluded: chain F residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN ** 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 = 0.3164 r_free = 0.3164 target = 0.034657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.025884 restraints weight = 102228.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.026381 restraints weight = 68169.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.026732 restraints weight = 51572.807| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7253 Z= 0.171 Angle : 0.716 12.057 9813 Z= 0.347 Chirality : 0.044 0.344 1171 Planarity : 0.004 0.034 1282 Dihedral : 4.154 16.251 995 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 3.14 % Allowed : 27.04 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.29), residues: 894 helix: 1.16 (0.25), residues: 439 sheet: -0.47 (0.58), residues: 76 loop : -0.76 (0.35), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.011 0.001 PHE B 234 TYR 0.013 0.001 TYR B 330 ARG 0.005 0.000 ARG E 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.14 seconds wall clock time: 48 minutes 8.48 seconds (2888.48 seconds total)