Starting phenix.real_space_refine on Wed Mar 4 19:01:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9m_25762/03_2026/7t9m_25762_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9m_25762/03_2026/7t9m_25762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t9m_25762/03_2026/7t9m_25762_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9m_25762/03_2026/7t9m_25762_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t9m_25762/03_2026/7t9m_25762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9m_25762/03_2026/7t9m_25762.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 5039 2.51 5 N 1255 2.21 5 O 1483 1.98 5 H 7719 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15546 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3219 Classifications: {'peptide': 217} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 205} Chain: "L" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3186 Classifications: {'peptide': 213} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "R" Number of atoms: 9071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 9071 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 27, 'TRANS': 537} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.92, per 1000 atoms: 0.19 Number of scatterers: 15546 At special positions: 0 Unit cell: (66.332, 131.376, 148.764, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 O 1483 8.00 N 1255 7.00 C 5039 6.00 H 7719 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 41 " distance=2.03 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.03 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN R 198 " " NAG R 801 " - " ASN R 177 " " NAG R 802 " - " ASN R 77 " " NAG R 803 " - " ASN R 113 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 485.7 milliseconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 16 sheets defined 30.3% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.663A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.761A pdb=" N THR H 139 " --> pdb=" O GLY H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 removed outlier: 3.879A pdb=" N SER H 168 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.997A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 181 through 188 removed outlier: 4.077A pdb=" N HIS L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 269 removed outlier: 4.134A pdb=" N SER R 268 " --> pdb=" O PRO R 264 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 264 through 269' Processing helix chain 'R' and resid 279 through 288 removed outlier: 4.467A pdb=" N CYS R 283 " --> pdb=" O TYR R 279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE R 286 " --> pdb=" O HIS R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 442 Processing helix chain 'R' and resid 447 through 477 Processing helix chain 'R' and resid 480 through 483 Processing helix chain 'R' and resid 484 through 491 Processing helix chain 'R' and resid 491 through 525 removed outlier: 3.684A pdb=" N ASN R 495 " --> pdb=" O GLY R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 534 through 555 removed outlier: 3.840A pdb=" N LEU R 555 " --> pdb=" O LEU R 551 " (cutoff:3.500A) Processing helix chain 'R' and resid 556 through 559 Processing helix chain 'R' and resid 576 through 610 Processing helix chain 'R' and resid 616 through 650 removed outlier: 3.974A pdb=" N ILE R 635 " --> pdb=" O PHE R 631 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N CYS R 636 " --> pdb=" O THR R 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET R 637 " --> pdb=" O ASP R 633 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA R 638 " --> pdb=" O PHE R 634 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 655 through 682 removed outlier: 4.031A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) Proline residue: R 668 - end of helix removed outlier: 4.606A pdb=" N SER R 671 " --> pdb=" O TYR R 667 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS R 672 " --> pdb=" O PRO R 668 " (cutoff:3.500A) Proline residue: R 675 - end of helix removed outlier: 3.669A pdb=" N THR R 682 " --> pdb=" O TYR R 678 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 693 removed outlier: 4.391A pdb=" N GLN R 686 " --> pdb=" O THR R 682 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.686A pdb=" N TYR H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.698A pdb=" N VAL H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.628A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.628A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 158 through 160 removed outlier: 3.667A pdb=" N LYS H 215 " --> pdb=" O CYS H 202 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 204 " --> pdb=" O VAL H 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.566A pdb=" N THR L 73 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.605A pdb=" N ASN L 52 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 115 through 117 removed outlier: 4.013A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 152 through 154 removed outlier: 3.631A pdb=" N ARG L 154 " --> pdb=" O TRP L 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP L 147 " --> pdb=" O ARG L 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 148 " --> pdb=" O THR L 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 56 through 58 removed outlier: 6.467A pdb=" N LEU R 57 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER R 84 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE R 81 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ARG R 109 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL R 83 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE R 154 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS R 183 " --> pdb=" O PHE R 154 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU R 156 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU R 180 " --> pdb=" O LEU R 202 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA R 204 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 66 through 67 removed outlier: 3.677A pdb=" N ILE R 67 " --> pdb=" O GLN R 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.188A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'R' and resid 166 through 167 removed outlier: 3.620A pdb=" N ILE R 167 " --> pdb=" O SER R 191 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 933 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: 3.54 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7705 1.02 - 1.22: 34 1.22 - 1.42: 3324 1.42 - 1.62: 4608 1.62 - 1.82: 68 Bond restraints: 15739 Sorted by residual: bond pdb=" ND2 ASN R 135 " pdb="HD21 ASN R 135 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" ND2 ASN R 135 " pdb="HD22 ASN R 135 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN R 650 " pdb="HD22 ASN R 650 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN R 650 " pdb="HD21 ASN R 650 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" N THR R 399 " pdb=" CA THR R 399 " ideal model delta sigma weight residual 1.463 1.504 -0.041 6.90e-03 2.10e+04 3.56e+01 ... (remaining 15734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 28204 3.28 - 6.56: 173 6.56 - 9.84: 21 9.84 - 13.12: 6 13.12 - 16.40: 8 Bond angle restraints: 28412 Sorted by residual: angle pdb=" N THR R 399 " pdb=" CA THR R 399 " pdb=" C THR R 399 " ideal model delta sigma weight residual 112.17 125.36 -13.19 1.36e+00 5.41e-01 9.40e+01 angle pdb=" C CYS R 398 " pdb=" N THR R 399 " pdb=" CA THR R 399 " ideal model delta sigma weight residual 119.83 128.18 -8.35 1.11e+00 8.12e-01 5.66e+01 angle pdb=" C TYR L 139 " pdb=" N PRO L 140 " pdb=" CA PRO L 140 " ideal model delta sigma weight residual 119.98 111.67 8.31 1.16e+00 7.43e-01 5.13e+01 angle pdb=" N TYR L 93 " pdb=" CA TYR L 93 " pdb=" C TYR L 93 " ideal model delta sigma weight residual 109.81 125.01 -15.20 2.21e+00 2.05e-01 4.73e+01 angle pdb=" N ASN L 137 " pdb=" CA ASN L 137 " pdb=" C ASN L 137 " ideal model delta sigma weight residual 111.24 120.27 -9.03 1.38e+00 5.25e-01 4.28e+01 ... (remaining 28407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6830 17.71 - 35.43: 599 35.43 - 53.14: 144 53.14 - 70.86: 34 70.86 - 88.57: 12 Dihedral angle restraints: 7619 sinusoidal: 4094 harmonic: 3525 Sorted by residual: dihedral pdb=" N TYR L 93 " pdb=" C TYR L 93 " pdb=" CA TYR L 93 " pdb=" CB TYR L 93 " ideal model delta harmonic sigma weight residual 122.80 150.70 -27.90 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" C TYR L 93 " pdb=" N TYR L 93 " pdb=" CA TYR L 93 " pdb=" CB TYR L 93 " ideal model delta harmonic sigma weight residual -122.60 -150.02 27.42 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" CB CYS R 494 " pdb=" SG CYS R 494 " pdb=" SG CYS R 569 " pdb=" CB CYS R 569 " ideal model delta sinusoidal sigma weight residual -86.00 -132.37 46.37 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 7616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 1282 0.256 - 0.513: 2 0.513 - 0.769: 2 0.769 - 1.025: 0 1.025 - 1.282: 1 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CA TYR L 93 " pdb=" N TYR L 93 " pdb=" C TYR L 93 " pdb=" CB TYR L 93 " both_signs ideal model delta sigma weight residual False 2.51 1.23 1.28 2.00e-01 2.50e+01 4.11e+01 chirality pdb=" CA TYR L 139 " pdb=" N TYR L 139 " pdb=" C TYR L 139 " pdb=" CB TYR L 139 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" CA THR R 399 " pdb=" N THR R 399 " pdb=" C THR R 399 " pdb=" CB THR R 399 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 1284 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 137 " -0.297 2.00e-02 2.50e+03 4.19e-01 2.64e+03 pdb=" CG ASN L 137 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN L 137 " 0.317 2.00e-02 2.50e+03 pdb=" ND2 ASN L 137 " -0.017 2.00e-02 2.50e+03 pdb="HD21 ASN L 137 " -0.677 2.00e-02 2.50e+03 pdb="HD22 ASN L 137 " 0.638 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 135 " -0.270 2.00e-02 2.50e+03 2.85e-01 1.22e+03 pdb=" CG ASN R 135 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN R 135 " 0.257 2.00e-02 2.50e+03 pdb=" ND2 ASN R 135 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN R 135 " 0.410 2.00e-02 2.50e+03 pdb="HD22 ASN R 135 " -0.423 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 650 " -0.087 2.00e-02 2.50e+03 8.51e-02 1.09e+02 pdb=" CG ASN R 650 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN R 650 " 0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN R 650 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN R 650 " 0.119 2.00e-02 2.50e+03 pdb="HD22 ASN R 650 " -0.122 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1372 2.23 - 2.82: 33260 2.82 - 3.41: 39682 3.41 - 4.01: 53816 4.01 - 4.60: 82035 Nonbonded interactions: 210165 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" H GLY L 100 " model vdw 1.637 2.450 nonbonded pdb=" OE1 GLU L 184 " pdb="HH12 ARG L 187 " model vdw 1.682 2.450 nonbonded pdb=" HG3 PRO L 8 " pdb=" HE2 MET L 11 " model vdw 1.696 2.440 nonbonded pdb=" OD1 ASP R 232 " pdb=" HG SER R 234 " model vdw 1.729 2.450 nonbonded pdb=" HE2 HIS H 35 " pdb=" OE1 GLU H 99 " model vdw 1.729 2.450 ... (remaining 210160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.030 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: 0.060 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.090 Find NCS groups from input model: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.005 0.066 8034 Z= 0.323 Angle : 0.879 15.204 10957 Z= 0.485 Chirality : 0.065 1.282 1287 Planarity : 0.005 0.065 1350 Dihedral : 12.803 88.199 2935 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.91 % Allowed : 0.79 % Favored : 98.30 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.27), residues: 987 helix: 1.73 (0.31), residues: 258 sheet: -0.33 (0.35), residues: 253 loop : -0.51 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 98 TYR 0.044 0.002 TYR L 93 PHE 0.022 0.001 PHE R 434 TRP 0.012 0.001 TRP R 546 HIS 0.002 0.001 HIS R 537 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 8020) covalent geometry : angle 0.87822 (10924) SS BOND : bond 0.00287 ( 9) SS BOND : angle 0.68222 ( 18) hydrogen bonds : bond 0.19251 ( 319) hydrogen bonds : angle 8.30444 ( 933) link_BETA1-4 : bond 0.00026 ( 1) link_BETA1-4 : angle 2.23211 ( 3) link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 1.30204 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.418 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.1751 time to fit residues: 22.0892 Evaluate side-chains 65 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 171 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 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 = 0.3953 r_free = 0.3953 target = 0.081979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.056997 restraints weight = 93668.008| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.87 r_work: 0.3068 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8034 Z= 0.187 Angle : 0.581 9.220 10957 Z= 0.305 Chirality : 0.042 0.298 1287 Planarity : 0.004 0.056 1350 Dihedral : 5.858 52.108 1176 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.57 % Allowed : 5.33 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.28), residues: 987 helix: 2.11 (0.32), residues: 257 sheet: -0.26 (0.35), residues: 258 loop : -0.30 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 49 TYR 0.037 0.001 TYR L 93 PHE 0.015 0.001 PHE R 434 TRP 0.004 0.001 TRP R 546 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8020) covalent geometry : angle 0.57871 (10924) SS BOND : bond 0.00422 ( 9) SS BOND : angle 0.72031 ( 18) hydrogen bonds : bond 0.04337 ( 319) hydrogen bonds : angle 5.99140 ( 933) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 1.56065 ( 3) link_NAG-ASN : bond 0.00311 ( 4) link_NAG-ASN : angle 1.28891 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.376 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: symmetry clash revert: symmetry clash REVERT: L 78 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8044 (mm-30) REVERT: L 93 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.6993 (t80) REVERT: R 666 PHE cc_start: 0.8390 (m-10) cc_final: 0.8183 (m-10) outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 0.1460 time to fit residues: 14.5588 Evaluate side-chains 62 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 239 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 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 = 0.3947 r_free = 0.3947 target = 0.081746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.056891 restraints weight = 93532.740| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.88 r_work: 0.3074 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8034 Z= 0.119 Angle : 0.520 8.975 10957 Z= 0.268 Chirality : 0.041 0.245 1287 Planarity : 0.004 0.037 1350 Dihedral : 5.175 53.218 1174 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.57 % Allowed : 5.67 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 987 helix: 2.31 (0.32), residues: 257 sheet: -0.32 (0.34), residues: 258 loop : -0.19 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 154 TYR 0.021 0.001 TYR L 93 PHE 0.014 0.001 PHE R 434 TRP 0.007 0.001 TRP R 546 HIS 0.003 0.000 HIS R 95 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8020) covalent geometry : angle 0.51862 (10924) SS BOND : bond 0.00332 ( 9) SS BOND : angle 0.55005 ( 18) hydrogen bonds : bond 0.03614 ( 319) hydrogen bonds : angle 5.36494 ( 933) link_BETA1-4 : bond 0.00027 ( 1) link_BETA1-4 : angle 1.44446 ( 3) link_NAG-ASN : bond 0.00110 ( 4) link_NAG-ASN : angle 0.93420 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.388 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 78 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8038 (mm-30) REVERT: L 144 ASN cc_start: 0.9422 (t0) cc_final: 0.9113 (t0) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.1414 time to fit residues: 14.1069 Evaluate side-chains 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 482 TYR Chi-restraints excluded: chain R residue 599 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 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 = 0.3922 r_free = 0.3922 target = 0.080264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.055242 restraints weight = 94325.603| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.81 r_work: 0.3029 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8034 Z= 0.205 Angle : 0.543 7.437 10957 Z= 0.281 Chirality : 0.041 0.237 1287 Planarity : 0.004 0.035 1350 Dihedral : 5.164 49.902 1174 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.91 % Allowed : 6.92 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.28), residues: 987 helix: 2.40 (0.32), residues: 257 sheet: -0.40 (0.34), residues: 259 loop : -0.22 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 154 TYR 0.024 0.001 TYR L 93 PHE 0.013 0.001 PHE R 634 TRP 0.005 0.001 TRP H 36 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 8020) covalent geometry : angle 0.54017 (10924) SS BOND : bond 0.00378 ( 9) SS BOND : angle 0.65004 ( 18) hydrogen bonds : bond 0.03362 ( 319) hydrogen bonds : angle 5.11558 ( 933) link_BETA1-4 : bond 0.00539 ( 1) link_BETA1-4 : angle 1.68111 ( 3) link_NAG-ASN : bond 0.00542 ( 4) link_NAG-ASN : angle 1.52984 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.434 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: symmetry clash REVERT: L 78 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8142 (mm-30) REVERT: L 93 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7174 (t80) REVERT: L 144 ASN cc_start: 0.9426 (t0) cc_final: 0.9128 (t0) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.1551 time to fit residues: 15.2604 Evaluate side-chains 62 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 482 TYR Chi-restraints excluded: chain R residue 599 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 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 = 0.3928 r_free = 0.3928 target = 0.080591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.055754 restraints weight = 93580.535| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.80 r_work: 0.3045 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8034 Z= 0.130 Angle : 0.499 6.972 10957 Z= 0.257 Chirality : 0.041 0.204 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.765 49.101 1174 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.91 % Allowed : 7.71 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.28), residues: 987 helix: 2.48 (0.31), residues: 257 sheet: -0.33 (0.34), residues: 258 loop : -0.14 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 154 TYR 0.016 0.001 TYR L 93 PHE 0.022 0.001 PHE R 416 TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8020) covalent geometry : angle 0.49814 (10924) SS BOND : bond 0.00300 ( 9) SS BOND : angle 0.50069 ( 18) hydrogen bonds : bond 0.03155 ( 319) hydrogen bonds : angle 4.89333 ( 933) link_BETA1-4 : bond 0.00133 ( 1) link_BETA1-4 : angle 1.47389 ( 3) link_NAG-ASN : bond 0.00107 ( 4) link_NAG-ASN : angle 0.94400 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.464 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: symmetry clash revert: symmetry clash REVERT: L 78 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8139 (mm-30) REVERT: L 144 ASN cc_start: 0.9410 (t0) cc_final: 0.9121 (t0) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 0.1335 time to fit residues: 13.0992 Evaluate side-chains 62 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 482 TYR Chi-restraints excluded: chain R residue 599 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN ** H 203 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 = 0.3916 r_free = 0.3916 target = 0.079878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055275 restraints weight = 93410.997| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.80 r_work: 0.3031 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8034 Z= 0.167 Angle : 0.510 7.484 10957 Z= 0.262 Chirality : 0.041 0.204 1287 Planarity : 0.003 0.035 1350 Dihedral : 4.738 46.250 1174 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.02 % Allowed : 7.94 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.28), residues: 987 helix: 2.54 (0.31), residues: 257 sheet: -0.23 (0.34), residues: 253 loop : -0.27 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 154 TYR 0.017 0.001 TYR L 93 PHE 0.011 0.001 PHE R 434 TRP 0.006 0.001 TRP H 36 HIS 0.002 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8020) covalent geometry : angle 0.50777 (10924) SS BOND : bond 0.00315 ( 9) SS BOND : angle 0.56879 ( 18) hydrogen bonds : bond 0.03109 ( 319) hydrogen bonds : angle 4.77197 ( 933) link_BETA1-4 : bond 0.00320 ( 1) link_BETA1-4 : angle 1.55954 ( 3) link_NAG-ASN : bond 0.00334 ( 4) link_NAG-ASN : angle 1.23951 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.374 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 78 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8222 (mm-30) REVERT: L 155 GLN cc_start: 0.8900 (pm20) cc_final: 0.8529 (mp10) REVERT: R 453 MET cc_start: 0.8951 (tpt) cc_final: 0.8425 (tmm) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.1349 time to fit residues: 13.0252 Evaluate side-chains 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 482 TYR Chi-restraints excluded: chain R residue 599 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 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 = 0.3923 r_free = 0.3923 target = 0.080101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.055635 restraints weight = 92227.811| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.80 r_work: 0.3053 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8034 Z= 0.108 Angle : 0.484 7.260 10957 Z= 0.247 Chirality : 0.041 0.176 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.485 44.944 1174 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.91 % Allowed : 8.05 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.28), residues: 987 helix: 2.59 (0.31), residues: 257 sheet: -0.16 (0.34), residues: 252 loop : -0.24 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 154 TYR 0.013 0.001 TYR L 93 PHE 0.011 0.001 PHE R 434 TRP 0.006 0.001 TRP H 36 HIS 0.001 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8020) covalent geometry : angle 0.48252 (10924) SS BOND : bond 0.00261 ( 9) SS BOND : angle 0.45622 ( 18) hydrogen bonds : bond 0.02972 ( 319) hydrogen bonds : angle 4.62421 ( 933) link_BETA1-4 : bond 0.00036 ( 1) link_BETA1-4 : angle 1.37909 ( 3) link_NAG-ASN : bond 0.00104 ( 4) link_NAG-ASN : angle 0.87047 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.391 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 78 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8214 (mm-30) REVERT: L 155 GLN cc_start: 0.8897 (pm20) cc_final: 0.8537 (mp10) REVERT: R 453 MET cc_start: 0.8931 (tpt) cc_final: 0.8402 (tmm) outliers start: 8 outliers final: 8 residues processed: 64 average time/residue: 0.1414 time to fit residues: 13.8191 Evaluate side-chains 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 451 PHE Chi-restraints excluded: chain R residue 482 TYR Chi-restraints excluded: chain R residue 599 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.080568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.056113 restraints weight = 92044.550| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.80 r_work: 0.3063 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8034 Z= 0.088 Angle : 0.474 8.001 10957 Z= 0.240 Chirality : 0.041 0.147 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.235 43.104 1174 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.68 % Allowed : 8.39 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.28), residues: 987 helix: 2.58 (0.31), residues: 260 sheet: -0.17 (0.34), residues: 255 loop : -0.17 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 154 TYR 0.010 0.001 TYR L 139 PHE 0.014 0.001 PHE R 666 TRP 0.006 0.001 TRP H 161 HIS 0.001 0.000 HIS R 95 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8020) covalent geometry : angle 0.47331 (10924) SS BOND : bond 0.00230 ( 9) SS BOND : angle 0.42971 ( 18) hydrogen bonds : bond 0.02829 ( 319) hydrogen bonds : angle 4.42450 ( 933) link_BETA1-4 : bond 0.00123 ( 1) link_BETA1-4 : angle 1.25375 ( 3) link_NAG-ASN : bond 0.00154 ( 4) link_NAG-ASN : angle 0.79611 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.425 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: symmetry clash revert: symmetry clash REVERT: L 78 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8194 (mm-30) REVERT: L 155 GLN cc_start: 0.8888 (pm20) cc_final: 0.8564 (mp10) REVERT: R 453 MET cc_start: 0.8927 (tpt) cc_final: 0.8361 (tmm) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.1417 time to fit residues: 13.6599 Evaluate side-chains 61 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 482 TYR Chi-restraints excluded: chain R residue 599 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 68 optimal weight: 0.3980 chunk 50 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 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 = 0.3943 r_free = 0.3943 target = 0.081162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.056541 restraints weight = 93112.361| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.81 r_work: 0.3076 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8034 Z= 0.089 Angle : 0.473 7.791 10957 Z= 0.240 Chirality : 0.040 0.141 1287 Planarity : 0.003 0.037 1350 Dihedral : 4.135 42.633 1174 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.57 % Allowed : 8.39 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.28), residues: 987 helix: 2.72 (0.31), residues: 257 sheet: -0.15 (0.34), residues: 255 loop : -0.23 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 154 TYR 0.010 0.001 TYR L 139 PHE 0.013 0.001 PHE R 666 TRP 0.007 0.001 TRP H 36 HIS 0.001 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8020) covalent geometry : angle 0.47235 (10924) SS BOND : bond 0.00237 ( 9) SS BOND : angle 0.45616 ( 18) hydrogen bonds : bond 0.02786 ( 319) hydrogen bonds : angle 4.31934 ( 933) link_BETA1-4 : bond 0.00128 ( 1) link_BETA1-4 : angle 1.23892 ( 3) link_NAG-ASN : bond 0.00123 ( 4) link_NAG-ASN : angle 0.80959 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.389 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.9080 (tt0) cc_final: 0.8797 (mt-10) REVERT: L 78 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8170 (mm-30) REVERT: L 155 GLN cc_start: 0.8898 (pm20) cc_final: 0.8569 (mp10) REVERT: R 453 MET cc_start: 0.8975 (tpt) cc_final: 0.8356 (tmm) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1536 time to fit residues: 14.0626 Evaluate side-chains 60 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 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 = 0.3929 r_free = 0.3929 target = 0.080924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.056446 restraints weight = 91897.327| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.73 r_work: 0.3063 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8034 Z= 0.105 Angle : 0.488 8.422 10957 Z= 0.245 Chirality : 0.040 0.141 1287 Planarity : 0.003 0.038 1350 Dihedral : 4.145 42.277 1174 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.68 % Allowed : 8.39 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.28), residues: 987 helix: 2.70 (0.31), residues: 260 sheet: -0.13 (0.34), residues: 255 loop : -0.20 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 528 TYR 0.011 0.001 TYR L 139 PHE 0.015 0.001 PHE R 666 TRP 0.005 0.001 TRP H 161 HIS 0.001 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8020) covalent geometry : angle 0.48726 (10924) SS BOND : bond 0.00247 ( 9) SS BOND : angle 0.48913 ( 18) hydrogen bonds : bond 0.02803 ( 319) hydrogen bonds : angle 4.27833 ( 933) link_BETA1-4 : bond 0.00007 ( 1) link_BETA1-4 : angle 1.28457 ( 3) link_NAG-ASN : bond 0.00116 ( 4) link_NAG-ASN : angle 0.90688 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.426 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.9045 (tt0) cc_final: 0.8780 (mt-10) REVERT: L 78 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8173 (mm-30) REVERT: R 453 MET cc_start: 0.8938 (tpt) cc_final: 0.8376 (tmm) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1422 time to fit residues: 13.1961 Evaluate side-chains 59 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 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 = 0.3917 r_free = 0.3917 target = 0.080259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055405 restraints weight = 91115.381| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.83 r_work: 0.3046 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8034 Z= 0.148 Angle : 0.504 8.143 10957 Z= 0.256 Chirality : 0.040 0.156 1287 Planarity : 0.003 0.038 1350 Dihedral : 4.257 41.590 1174 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.68 % Allowed : 8.73 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.28), residues: 987 helix: 2.68 (0.31), residues: 259 sheet: -0.16 (0.34), residues: 255 loop : -0.21 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 154 TYR 0.012 0.001 TYR L 93 PHE 0.016 0.001 PHE R 666 TRP 0.003 0.001 TRP R 488 HIS 0.002 0.000 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8020) covalent geometry : angle 0.50201 (10924) SS BOND : bond 0.00280 ( 9) SS BOND : angle 0.53538 ( 18) hydrogen bonds : bond 0.02884 ( 319) hydrogen bonds : angle 4.33507 ( 933) link_BETA1-4 : bond 0.00132 ( 1) link_BETA1-4 : angle 1.44656 ( 3) link_NAG-ASN : bond 0.00244 ( 4) link_NAG-ASN : angle 1.05828 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4389.57 seconds wall clock time: 74 minutes 59.34 seconds (4499.34 seconds total)