Starting phenix.real_space_refine on Sat Jun 14 03:34:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9m_25762/06_2025/7t9m_25762_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9m_25762/06_2025/7t9m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9m_25762/06_2025/7t9m_25762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9m_25762/06_2025/7t9m_25762.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9m_25762/06_2025/7t9m_25762_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9m_25762/06_2025/7t9m_25762_neut_trim.cif" } resolution = 3.1 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= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.67, per 1000 atoms: 0.56 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: 3.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.43 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: 5.52 Time building geometry restraints manager: 4.36 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: 85.360 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: 0.280 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.680 ------------------------------------------------------------------------------- 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 (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: 0.15 (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 TRP 0.012 0.001 TRP R 546 HIS 0.002 0.001 HIS R 537 PHE 0.022 0.001 PHE R 434 TYR 0.044 0.002 TYR L 93 ARG 0.003 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 1.30204 ( 12) link_BETA1-4 : bond 0.00026 ( 1) link_BETA1-4 : angle 2.23211 ( 3) hydrogen bonds : bond 0.19251 ( 319) hydrogen bonds : angle 8.30444 ( 933) SS BOND : bond 0.00287 ( 9) SS BOND : angle 0.68222 ( 18) covalent geometry : bond 0.00544 ( 8020) covalent geometry : angle 0.87822 (10924) *********************** 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 : 1.612 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 outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.3863 time to fit residues: 48.5610 Evaluate side-chains 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 82 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.081824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.056780 restraints weight = 92983.640| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.90 r_work: 0.3071 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1685 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= 0.195 Angle : 0.587 9.319 10957 Z= 0.309 Chirality : 0.042 0.281 1287 Planarity : 0.004 0.058 1350 Dihedral : 5.889 53.945 1176 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.57 % Allowed : 5.56 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.44 (0.28), residues: 987 helix: 2.09 (0.32), residues: 257 sheet: -0.31 (0.34), residues: 260 loop : -0.29 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 36 HIS 0.003 0.001 HIS L 91 PHE 0.014 0.001 PHE R 666 TYR 0.035 0.001 TYR L 93 ARG 0.004 0.000 ARG L 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 4) link_NAG-ASN : angle 1.35500 ( 12) link_BETA1-4 : bond 0.00421 ( 1) link_BETA1-4 : angle 1.65924 ( 3) hydrogen bonds : bond 0.04013 ( 319) hydrogen bonds : angle 5.92892 ( 933) SS BOND : bond 0.00438 ( 9) SS BOND : angle 0.74238 ( 18) covalent geometry : bond 0.00427 ( 8020) covalent geometry : angle 0.58477 (10924) *********************** 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 65 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 1.145 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: 0.8312 (mm-30) cc_final: 0.8062 (mm-30) REVERT: L 93 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6983 (t80) REVERT: R 666 PHE cc_start: 0.8404 (m-10) cc_final: 0.8191 (m-10) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.3256 time to fit residues: 31.3630 Evaluate side-chains 63 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 0.0060 chunk 49 optimal weight: 2.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- 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 = 0.082052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057194 restraints weight = 92784.484| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.86 r_work: 0.3083 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8034 Z= 0.103 Angle : 0.513 9.043 10957 Z= 0.264 Chirality : 0.041 0.233 1287 Planarity : 0.004 0.038 1350 Dihedral : 5.103 53.768 1174 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.45 % Allowed : 5.67 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.61 (0.28), residues: 987 helix: 2.29 (0.32), residues: 257 sheet: -0.27 (0.34), residues: 257 loop : -0.18 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 546 HIS 0.002 0.000 HIS R 95 PHE 0.014 0.001 PHE R 434 TYR 0.018 0.001 TYR L 93 ARG 0.002 0.000 ARG L 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 4) link_NAG-ASN : angle 0.83587 ( 12) link_BETA1-4 : bond 0.00104 ( 1) link_BETA1-4 : angle 1.35965 ( 3) hydrogen bonds : bond 0.03617 ( 319) hydrogen bonds : angle 5.33602 ( 933) SS BOND : bond 0.00311 ( 9) SS BOND : angle 0.51334 ( 18) covalent geometry : bond 0.00232 ( 8020) covalent geometry : angle 0.51180 (10924) *********************** 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: 4 poor density : 61 time to evaluate : 3.164 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: 0.8307 (mm-30) cc_final: 0.8032 (mm-30) REVERT: L 144 ASN cc_start: 0.9409 (t0) cc_final: 0.9110 (t0) REVERT: R 38 ARG cc_start: 0.8584 (mmt90) cc_final: 0.8378 (ttp80) outliers start: 4 outliers final: 4 residues processed: 65 average time/residue: 0.4888 time to fit residues: 50.1670 Evaluate side-chains 63 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 599 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.080998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.055903 restraints weight = 93291.794| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.81 r_work: 0.3052 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8034 Z= 0.171 Angle : 0.521 6.817 10957 Z= 0.269 Chirality : 0.041 0.220 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.984 51.438 1174 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.79 % Allowed : 6.46 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.68 (0.28), residues: 987 helix: 2.45 (0.32), residues: 257 sheet: -0.30 (0.34), residues: 258 loop : -0.15 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 36 HIS 0.002 0.001 HIS L 91 PHE 0.013 0.001 PHE R 434 TYR 0.021 0.001 TYR L 93 ARG 0.002 0.000 ARG L 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 4) link_NAG-ASN : angle 1.36804 ( 12) link_BETA1-4 : bond 0.00325 ( 1) link_BETA1-4 : angle 1.54424 ( 3) hydrogen bonds : bond 0.03240 ( 319) hydrogen bonds : angle 5.04133 ( 933) SS BOND : bond 0.00340 ( 9) SS BOND : angle 0.61887 ( 18) covalent geometry : bond 0.00381 ( 8020) covalent geometry : angle 0.51825 (10924) *********************** 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 65 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.935 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 78 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8070 (mm-30) REVERT: L 144 ASN cc_start: 0.9433 (t0) cc_final: 0.9144 (t0) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.4363 time to fit residues: 42.8966 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 : 1.844 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 599 CYS Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.080686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.055709 restraints weight = 94461.685| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.82 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: 0.8030 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8034 Z= 0.156 Angle : 0.508 7.748 10957 Z= 0.261 Chirality : 0.041 0.209 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.773 49.521 1174 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.79 % Allowed : 7.37 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.72 (0.28), residues: 987 helix: 2.49 (0.31), residues: 257 sheet: -0.27 (0.34), residues: 258 loop : -0.14 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS L 91 PHE 0.023 0.001 PHE R 416 TYR 0.019 0.001 TYR R 466 ARG 0.002 0.000 ARG L 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 4) link_NAG-ASN : angle 1.06346 ( 12) link_BETA1-4 : bond 0.00249 ( 1) link_BETA1-4 : angle 1.53241 ( 3) hydrogen bonds : bond 0.03196 ( 319) hydrogen bonds : angle 4.87558 ( 933) SS BOND : bond 0.00318 ( 9) SS BOND : angle 0.55467 ( 18) covalent geometry : bond 0.00348 ( 8020) covalent geometry : angle 0.50601 (10924) *********************** 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 63 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.177 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: 0.8358 (mm-30) cc_final: 0.8123 (mm-30) REVERT: L 144 ASN cc_start: 0.9410 (t0) cc_final: 0.9125 (t0) REVERT: R 453 MET cc_start: 0.8999 (tpt) cc_final: 0.8407 (tmm) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.3356 time to fit residues: 30.9257 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 : 1.228 ------------------------------------------------------------------------------- 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 599 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 26 optimal weight: 0.0030 chunk 52 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.080135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055561 restraints weight = 92366.215| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.80 r_work: 0.3050 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8034 Z= 0.136 Angle : 0.493 8.230 10957 Z= 0.252 Chirality : 0.041 0.187 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.599 47.380 1174 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.68 % Allowed : 7.71 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.77 (0.28), residues: 987 helix: 2.56 (0.31), residues: 257 sheet: -0.16 (0.34), residues: 253 loop : -0.19 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS L 91 PHE 0.011 0.001 PHE R 434 TYR 0.015 0.001 TYR L 93 ARG 0.002 0.000 ARG L 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 4) link_NAG-ASN : angle 1.02703 ( 12) link_BETA1-4 : bond 0.00052 ( 1) link_BETA1-4 : angle 1.48452 ( 3) hydrogen bonds : bond 0.03016 ( 319) hydrogen bonds : angle 4.68331 ( 933) SS BOND : bond 0.00289 ( 9) SS BOND : angle 0.51296 ( 18) covalent geometry : bond 0.00307 ( 8020) covalent geometry : angle 0.49162 (10924) *********************** 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 65 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.335 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: 0.8414 (mm-30) cc_final: 0.8162 (mm-30) REVERT: R 453 MET cc_start: 0.8960 (tpt) cc_final: 0.8337 (tmm) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.3360 time to fit residues: 32.3513 Evaluate side-chains 63 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 599 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 83 optimal weight: 0.1980 chunk 84 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.080224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.055704 restraints weight = 92699.057| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.82 r_work: 0.3054 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8034 Z= 0.115 Angle : 0.487 8.730 10957 Z= 0.248 Chirality : 0.040 0.170 1287 Planarity : 0.003 0.037 1350 Dihedral : 4.428 45.126 1174 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.68 % Allowed : 7.82 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.77 (0.28), residues: 987 helix: 2.58 (0.31), residues: 257 sheet: -0.16 (0.34), residues: 255 loop : -0.19 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.001 0.000 HIS L 91 PHE 0.011 0.001 PHE R 416 TYR 0.012 0.001 TYR L 93 ARG 0.002 0.000 ARG L 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 4) link_NAG-ASN : angle 0.91259 ( 12) link_BETA1-4 : bond 0.00003 ( 1) link_BETA1-4 : angle 1.42508 ( 3) hydrogen bonds : bond 0.02970 ( 319) hydrogen bonds : angle 4.55438 ( 933) SS BOND : bond 0.00269 ( 9) SS BOND : angle 0.48351 ( 18) covalent geometry : bond 0.00260 ( 8020) covalent geometry : angle 0.48623 (10924) *********************** 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 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 1.309 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: 0.8425 (mm-30) cc_final: 0.8189 (mm-30) REVERT: R 453 MET cc_start: 0.8902 (tpt) cc_final: 0.8334 (tmm) outliers start: 6 outliers final: 6 residues processed: 63 average time/residue: 0.3419 time to fit residues: 32.6513 Evaluate side-chains 63 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 599 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.080129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.055733 restraints weight = 92766.588| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.77 r_work: 0.3051 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8034 Z= 0.135 Angle : 0.490 7.756 10957 Z= 0.250 Chirality : 0.040 0.173 1287 Planarity : 0.003 0.037 1350 Dihedral : 4.414 43.436 1174 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.79 % Allowed : 7.71 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.79 (0.28), residues: 987 helix: 2.63 (0.31), residues: 257 sheet: -0.16 (0.34), residues: 255 loop : -0.20 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS L 91 PHE 0.012 0.001 PHE R 666 TYR 0.014 0.001 TYR L 93 ARG 0.002 0.000 ARG L 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 4) link_NAG-ASN : angle 1.03170 ( 12) link_BETA1-4 : bond 0.00138 ( 1) link_BETA1-4 : angle 1.45451 ( 3) hydrogen bonds : bond 0.02937 ( 319) hydrogen bonds : angle 4.50303 ( 933) SS BOND : bond 0.00274 ( 9) SS BOND : angle 0.50984 ( 18) covalent geometry : bond 0.00305 ( 8020) covalent geometry : angle 0.48849 (10924) *********************** 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: 7 poor density : 57 time to evaluate : 1.320 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: 0.8408 (mm-30) cc_final: 0.8183 (mm-30) REVERT: R 453 MET cc_start: 0.8907 (tpt) cc_final: 0.8345 (tmm) outliers start: 7 outliers final: 7 residues processed: 62 average time/residue: 0.3382 time to fit residues: 31.8551 Evaluate side-chains 63 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 599 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.080470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.055641 restraints weight = 92379.766| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.76 r_work: 0.3042 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8034 Z= 0.124 Angle : 0.489 8.431 10957 Z= 0.249 Chirality : 0.040 0.162 1287 Planarity : 0.003 0.038 1350 Dihedral : 4.339 42.664 1174 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.68 % Allowed : 8.05 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.77 (0.28), residues: 987 helix: 2.62 (0.31), residues: 259 sheet: -0.18 (0.34), residues: 255 loop : -0.22 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.004 0.000 HIS R 32 PHE 0.014 0.001 PHE R 666 TYR 0.011 0.001 TYR L 139 ARG 0.005 0.000 ARG R 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 4) link_NAG-ASN : angle 0.92857 ( 12) link_BETA1-4 : bond 0.00032 ( 1) link_BETA1-4 : angle 1.43309 ( 3) hydrogen bonds : bond 0.02895 ( 319) hydrogen bonds : angle 4.43507 ( 933) SS BOND : bond 0.00266 ( 9) SS BOND : angle 0.48935 ( 18) covalent geometry : bond 0.00282 ( 8020) covalent geometry : angle 0.48761 (10924) *********************** 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 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 1.255 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: 0.8403 (mm-30) cc_final: 0.8182 (mm-30) REVERT: R 453 MET cc_start: 0.8954 (tpt) cc_final: 0.8391 (tmm) outliers start: 6 outliers final: 6 residues processed: 63 average time/residue: 0.3266 time to fit residues: 32.9413 Evaluate side-chains 61 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 599 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.080401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.055655 restraints weight = 92615.205| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.82 r_work: 0.3040 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8034 Z= 0.133 Angle : 0.501 8.741 10957 Z= 0.254 Chirality : 0.040 0.162 1287 Planarity : 0.003 0.037 1350 Dihedral : 4.343 42.097 1174 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.79 % Allowed : 8.05 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.78 (0.28), residues: 987 helix: 2.64 (0.31), residues: 259 sheet: -0.19 (0.34), residues: 255 loop : -0.22 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS L 91 PHE 0.015 0.001 PHE R 666 TYR 0.012 0.001 TYR L 93 ARG 0.003 0.000 ARG L 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 4) link_NAG-ASN : angle 0.99570 ( 12) link_BETA1-4 : bond 0.00102 ( 1) link_BETA1-4 : angle 1.44631 ( 3) hydrogen bonds : bond 0.02891 ( 319) hydrogen bonds : angle 4.41816 ( 933) SS BOND : bond 0.00272 ( 9) SS BOND : angle 0.49862 ( 18) covalent geometry : bond 0.00302 ( 8020) covalent geometry : angle 0.49995 (10924) ********************** 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: 7 poor density : 55 time to evaluate : 1.273 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: 0.8421 (mm-30) cc_final: 0.8214 (mm-30) REVERT: R 453 MET cc_start: 0.8952 (tpt) cc_final: 0.8400 (tmm) outliers start: 7 outliers final: 7 residues processed: 60 average time/residue: 0.3042 time to fit residues: 28.9741 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 : 1.167 ------------------------------------------------------------------------------- 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 599 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3920 r_free = 0.3920 target = 0.080396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.055559 restraints weight = 91820.389| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.83 r_work: 0.3047 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8034 Z= 0.119 Angle : 0.496 8.320 10957 Z= 0.252 Chirality : 0.040 0.152 1287 Planarity : 0.003 0.038 1350 Dihedral : 4.277 41.690 1174 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.74 (0.28), residues: 987 helix: 2.58 (0.31), residues: 259 sheet: -0.18 (0.34), residues: 255 loop : -0.24 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS L 91 PHE 0.015 0.001 PHE R 666 TYR 0.011 0.001 TYR L 139 ARG 0.002 0.000 ARG L 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 4) link_NAG-ASN : angle 0.89814 ( 12) link_BETA1-4 : bond 0.00069 ( 1) link_BETA1-4 : angle 1.39477 ( 3) hydrogen bonds : bond 0.02890 ( 319) hydrogen bonds : angle 4.38799 ( 933) SS BOND : bond 0.00261 ( 9) SS BOND : angle 0.47953 ( 18) covalent geometry : bond 0.00273 ( 8020) covalent geometry : angle 0.49463 (10924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9466.43 seconds wall clock time: 164 minutes 24.63 seconds (9864.63 seconds total)