Starting phenix.real_space_refine on Wed Feb 12 04:40:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umx_42387/02_2025/8umx_42387.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umx_42387/02_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_42387/02_2025/8umx_42387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umx_42387/02_2025/8umx_42387.map" model { file = "/net/cci-nas-00/data/ceres_data/8umx_42387/02_2025/8umx_42387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umx_42387/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.90, per 1000 atoms: 0.96 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: 1.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.73 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: 2.02 Time building geometry restraints manager: 1.89 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: 11.010 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.580 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- 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 : 0.906 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: 0.2062 time to fit residues: 14.3560 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 : 0.802 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025878 restraints weight = 101214.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.026338 restraints weight = 69533.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026591 restraints weight = 53755.739| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.887 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: 0.7869 (tpt) cc_final: 0.7142 (tpt) REVERT: B 113 MET cc_start: 0.8255 (pmm) cc_final: 0.7610 (pmm) REVERT: B 158 MET cc_start: 0.8592 (ptp) cc_final: 0.8341 (ppp) REVERT: C 157 MET cc_start: 0.9193 (ptm) cc_final: 0.8913 (ptp) REVERT: F 67 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8407 (pt0) outliers start: 38 outliers final: 17 residues processed: 83 average time/residue: 0.1870 time to fit residues: 21.7916 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 : 0.908 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 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 = 0.3132 r_free = 0.3132 target = 0.033911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.024860 restraints weight = 102125.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.025322 restraints weight = 69273.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.025642 restraints weight = 53034.247| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7253 Z= 0.302 Angle : 0.679 6.839 9813 Z= 0.353 Chirality : 0.043 0.193 1171 Planarity : 0.005 0.056 1282 Dihedral : 5.006 55.234 999 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 5.41 % Allowed : 23.40 % 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 (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: -0.23 (0.29), residues: 894 helix: 1.03 (0.25), residues: 436 sheet: -1.39 (0.51), residues: 91 loop : -1.24 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 246 HIS 0.008 0.001 HIS C 241 PHE 0.012 0.002 PHE B 59 TYR 0.014 0.002 TYR C 313 ARG 0.009 0.001 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 85 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 42 time to evaluate : 0.797 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: 0.8179 (tpt) cc_final: 0.7542 (tpt) REVERT: B 113 MET cc_start: 0.8420 (pmm) cc_final: 0.8087 (pmm) REVERT: B 206 MET cc_start: 0.7745 (mmm) cc_final: 0.7527 (mmm) REVERT: C 157 MET cc_start: 0.9228 (ptm) cc_final: 0.9003 (ptp) outliers start: 43 outliers final: 24 residues processed: 83 average time/residue: 0.1943 time to fit residues: 22.0134 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 : 0.686 ------------------------------------------------------------------------------- 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 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 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 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 114 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 135 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.3980 chunk 4 optimal weight: 0.0670 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 1.2920 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.034287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025130 restraints weight = 102724.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.025640 restraints weight = 67764.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.025992 restraints weight = 51071.383| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2331 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= 0.177 Angle : 0.631 10.328 9813 Z= 0.319 Chirality : 0.043 0.197 1171 Planarity : 0.004 0.048 1282 Dihedral : 4.843 57.170 999 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 4.91 % Allowed : 23.77 % 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: -0.08 (0.29), residues: 894 helix: 1.14 (0.25), residues: 438 sheet: -1.25 (0.51), residues: 90 loop : -1.18 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 246 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 0.007 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 83 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 44 time to evaluate : 0.912 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: symmetry clash REVERT: B 1 MET cc_start: 0.8455 (tpt) cc_final: 0.7888 (tpt) REVERT: B 113 MET cc_start: 0.8764 (pmm) cc_final: 0.8491 (pmm) REVERT: B 206 MET cc_start: 0.7782 (mmm) cc_final: 0.7550 (mmm) REVERT: C 157 MET cc_start: 0.9323 (ptm) cc_final: 0.9056 (ptp) REVERT: C 223 MET cc_start: 0.9483 (mmm) cc_final: 0.8733 (mmm) REVERT: D 71 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8770 (m) outliers start: 39 outliers final: 22 residues processed: 80 average time/residue: 0.2106 time to fit residues: 22.9586 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 : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ARG Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain C residue 36 ARG 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 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 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 122 ILE 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: 3.9990 chunk 56 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 101 ASN C 103 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.034361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.025200 restraints weight = 99415.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.025717 restraints weight = 66625.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.026059 restraints weight = 50496.831| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2528 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= 0.170 Angle : 0.644 10.547 9813 Z= 0.319 Chirality : 0.043 0.153 1171 Planarity : 0.004 0.045 1282 Dihedral : 4.761 57.845 999 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 4.03 % Allowed : 24.65 % 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: -0.06 (0.29), residues: 894 helix: 1.16 (0.25), residues: 436 sheet: -1.20 (0.51), residues: 90 loop : -1.17 (0.35), residues: 368 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 0.008 0.001 TYR C 313 ARG 0.005 0.000 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 74 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 42 time to evaluate : 0.857 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: 0.8483 (tpt) cc_final: 0.7926 (tpt) REVERT: B 71 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 113 MET cc_start: 0.8799 (pmm) cc_final: 0.8553 (pmm) REVERT: B 206 MET cc_start: 0.7814 (mmm) cc_final: 0.7556 (mmm) REVERT: B 330 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8220 (t80) REVERT: C 108 LYS cc_start: 0.9626 (mmtt) cc_final: 0.9216 (mmtm) REVERT: C 157 MET cc_start: 0.9317 (ptm) cc_final: 0.9064 (ptp) REVERT: C 223 MET cc_start: 0.9571 (mmm) cc_final: 0.8803 (mmm) REVERT: D 71 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8759 (m) outliers start: 32 outliers final: 22 residues processed: 71 average time/residue: 0.2168 time to fit residues: 20.8770 Evaluate side-chains 66 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.034473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.025370 restraints weight = 100567.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.025873 restraints weight = 68325.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.026208 restraints weight = 52288.449| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7253 Z= 0.163 Angle : 0.643 11.008 9813 Z= 0.317 Chirality : 0.043 0.206 1171 Planarity : 0.004 0.039 1282 Dihedral : 4.634 58.904 999 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 4.53 % Allowed : 24.40 % Favored : 71.07 % 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: 0.17 (0.29), residues: 894 helix: 1.26 (0.25), residues: 437 sheet: -0.91 (0.56), residues: 76 loop : -1.01 (0.34), residues: 381 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 0.004 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 81 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 45 time to evaluate : 0.860 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: 0.8571 (tpt) cc_final: 0.8045 (tpt) REVERT: B 71 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7606 (tp) REVERT: B 113 MET cc_start: 0.8795 (pmm) cc_final: 0.8574 (pmm) REVERT: B 206 MET cc_start: 0.7842 (mmm) cc_final: 0.7552 (mmm) REVERT: B 330 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8028 (t80) REVERT: C 108 LYS cc_start: 0.9657 (mmtt) cc_final: 0.9208 (mmtm) REVERT: C 157 MET cc_start: 0.9305 (ptm) cc_final: 0.9057 (ptp) REVERT: C 223 MET cc_start: 0.9551 (mmm) cc_final: 0.8690 (mmm) REVERT: D 71 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8951 (m) REVERT: D 98 ASP cc_start: 0.9067 (t0) cc_final: 0.8681 (t0) outliers start: 36 outliers final: 22 residues processed: 78 average time/residue: 0.1935 time to fit residues: 20.7637 Evaluate side-chains 66 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN A 534 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.034507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.025463 restraints weight = 101451.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.025955 restraints weight = 69242.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.026281 restraints weight = 52721.063| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2864 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= 0.168 Angle : 0.667 10.816 9813 Z= 0.328 Chirality : 0.042 0.174 1171 Planarity : 0.004 0.047 1282 Dihedral : 4.584 55.405 999 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.97 % 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 (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: 0.21 (0.29), residues: 894 helix: 1.26 (0.25), residues: 438 sheet: -0.81 (0.57), residues: 76 loop : -0.96 (0.34), residues: 380 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 0.004 0.000 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 74 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 0.887 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: 0.8697 (ppp) cc_final: 0.8368 (tmm) REVERT: A 539 MET cc_start: 0.8578 (ptm) cc_final: 0.8349 (ptt) REVERT: B 1 MET cc_start: 0.8019 (tpt) cc_final: 0.7358 (tpt) REVERT: B 71 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7603 (tp) REVERT: B 113 MET cc_start: 0.8406 (pmm) cc_final: 0.8206 (pmm) REVERT: B 206 MET cc_start: 0.7863 (mmm) cc_final: 0.7532 (mmm) REVERT: B 330 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7861 (t80) REVERT: C 108 LYS cc_start: 0.9655 (mmtt) cc_final: 0.9229 (mmtm) REVERT: C 223 MET cc_start: 0.9349 (mmm) cc_final: 0.8578 (mmm) REVERT: D 71 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8574 (m) REVERT: D 98 ASP cc_start: 0.8819 (t0) cc_final: 0.8337 (t0) outliers start: 31 outliers final: 25 residues processed: 73 average time/residue: 0.2215 time to fit residues: 21.9889 Evaluate side-chains 68 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 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 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 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 17 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.034315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.025384 restraints weight = 102084.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.025869 restraints weight = 68594.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.026171 restraints weight = 52339.647| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2998 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= 0.179 Angle : 0.680 10.875 9813 Z= 0.336 Chirality : 0.044 0.350 1171 Planarity : 0.004 0.042 1282 Dihedral : 4.585 55.719 999 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % 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 (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: 1.30 (0.25), residues: 438 sheet: -0.73 (0.57), residues: 76 loop : -0.92 (0.34), residues: 380 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 0.010 0.001 PHE B 234 TYR 0.006 0.001 TYR C 313 ARG 0.006 0.000 ARG E 70 *********************** 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 71 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 40 time to evaluate : 0.935 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: 0.8664 (ppp) cc_final: 0.8430 (tmm) REVERT: B 1 MET cc_start: 0.8004 (tpt) cc_final: 0.7326 (tpt) REVERT: B 71 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7621 (tp) REVERT: B 330 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7856 (t80) REVERT: C 108 LYS cc_start: 0.9648 (mmtt) cc_final: 0.9230 (mmtm) REVERT: C 223 MET cc_start: 0.9379 (mmm) cc_final: 0.8655 (mmm) REVERT: D 71 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8430 (m) REVERT: D 98 ASP cc_start: 0.8810 (t0) cc_final: 0.8312 (t0) outliers start: 31 outliers final: 26 residues processed: 70 average time/residue: 0.2036 time to fit residues: 19.6466 Evaluate side-chains 69 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 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 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 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 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 34 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.034478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.025592 restraints weight = 102349.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.026094 restraints weight = 68552.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.026426 restraints weight = 52023.778| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3099 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= 0.176 Angle : 0.688 11.277 9813 Z= 0.337 Chirality : 0.044 0.306 1171 Planarity : 0.004 0.036 1282 Dihedral : 4.560 57.011 999 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 4.28 % Allowed : 25.79 % 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: 0.31 (0.29), residues: 894 helix: 1.28 (0.25), residues: 438 sheet: -0.57 (0.58), residues: 76 loop : -0.87 (0.34), residues: 380 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 75 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 41 time to evaluate : 0.908 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: 0.8549 (tpt) cc_final: 0.7878 (tpt) REVERT: B 330 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8154 (t80) REVERT: C 108 LYS cc_start: 0.9709 (mmtt) cc_final: 0.9447 (mmtm) REVERT: C 223 MET cc_start: 0.9601 (mmm) cc_final: 0.8820 (mmm) REVERT: D 98 ASP cc_start: 0.9055 (t0) cc_final: 0.8611 (t0) REVERT: E 58 MET cc_start: 0.8392 (mpp) cc_final: 0.8086 (mmm) outliers start: 34 outliers final: 28 residues processed: 74 average time/residue: 0.1992 time to fit residues: 20.3287 Evaluate side-chains 69 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 52 GLN 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 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 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 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 76 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** D 102 ASN ** 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 = 0.034065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.025280 restraints weight = 104736.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.025773 restraints weight = 69647.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.026084 restraints weight = 52779.632| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7253 Z= 0.218 Angle : 0.711 12.637 9813 Z= 0.350 Chirality : 0.044 0.339 1171 Planarity : 0.004 0.033 1282 Dihedral : 4.691 59.085 999 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % Rotamer: Outliers : 3.77 % Allowed : 25.79 % 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: 0.34 (0.29), residues: 894 helix: 1.20 (0.25), residues: 442 sheet: -0.65 (0.57), residues: 77 loop : -0.72 (0.35), residues: 375 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 0.009 0.001 PHE B 236 TYR 0.009 0.001 TYR C 313 ARG 0.006 0.001 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 69 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.837 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: 0.8582 (tpt) cc_final: 0.7891 (tpt) REVERT: B 112 PHE cc_start: 0.9483 (m-10) cc_final: 0.9222 (m-80) REVERT: B 330 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8346 (t80) REVERT: C 108 LYS cc_start: 0.9713 (mmtt) cc_final: 0.9401 (mmtm) REVERT: C 223 MET cc_start: 0.9597 (mmm) cc_final: 0.8551 (mmm) REVERT: D 71 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8873 (m) REVERT: D 98 ASP cc_start: 0.9067 (t0) cc_final: 0.8621 (t0) REVERT: E 58 MET cc_start: 0.8567 (mpp) cc_final: 0.8074 (mmm) outliers start: 30 outliers final: 27 residues processed: 68 average time/residue: 0.1982 time to fit residues: 18.5689 Evaluate side-chains 68 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 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 64 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 122 ILE 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 1 optimal weight: 7.9990 chunk 72 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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 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 = 0.3144 r_free = 0.3144 target = 0.034054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.025315 restraints weight = 103663.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.025812 restraints weight = 68676.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.026112 restraints weight = 51871.861| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7253 Z= 0.212 Angle : 0.738 12.147 9813 Z= 0.366 Chirality : 0.044 0.338 1171 Planarity : 0.004 0.033 1282 Dihedral : 4.637 58.132 999 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer: Outliers : 3.77 % Allowed : 26.04 % 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: 0.35 (0.29), residues: 894 helix: 1.21 (0.25), residues: 440 sheet: -0.60 (0.58), residues: 77 loop : -0.69 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 246 HIS 0.007 0.001 HIS C 241 PHE 0.009 0.001 PHE B 234 TYR 0.008 0.001 TYR C 313 ARG 0.005 0.000 ARG A 535 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.33 seconds wall clock time: 50 minutes 0.74 seconds (3000.74 seconds total)