Starting phenix.real_space_refine on Fri Sep 11 04:29:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cx0_27032/09_2026/8cx0_27032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx0_27032/09_2026/8cx0_27032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cx0_27032/09_2026/8cx0_27032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx0_27032/09_2026/8cx0_27032.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8cx0_27032/09_2026/8cx0_27032.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cx0_27032/09_2026/8cx0_27032.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cx0_27032/09_2026/8cx0_27032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx0_27032/09_2026/8cx0_27032.cif" } resolution = 2.7 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= 0.028 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 8 5.49 5 S 47 5.16 5 C 4798 2.51 5 N 1346 2.21 5 O 1373 1.98 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7575 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3200 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1468 Classifications: {'peptide': 176} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 166} Chain: "C" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1276 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "D" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "E" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain breaks: 1 Chain: "K" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 4} Link IDs: {'rna2p': 3, 'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 288 20.523 21.995 37.524 1.00 61.84 S ATOM 2469 SG CYS A 291 21.392 24.957 38.126 1.00 56.62 S ATOM 813 SG CYS A 97 41.384 56.405 50.521 1.00 39.00 S ATOM 835 SG CYS A 100 44.558 55.360 52.399 1.00 42.31 S ATOM 4184 SG CYS B 114 18.078 86.830 54.083 1.00 63.17 S ATOM 4328 SG CYS B 133 21.300 85.170 55.518 1.00 67.06 S Time building chain proxies: 1.52, per 1000 atoms: 0.20 Number of scatterers: 7575 At special positions: 0 Unit cell: (80.16, 141.115, 86.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 47 16.00 P 8 15.00 O 1373 8.00 N 1346 7.00 C 4798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 414.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 257 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 288 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 291 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 65 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 100 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 139 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 108 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 133 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 114 " Number of angles added : 2 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 40.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.522A pdb=" N LYS A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 153 through 165 removed outlier: 3.840A pdb=" N VAL A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 267 through 270 removed outlier: 3.513A pdb=" N LYS A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 270' Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.844A pdb=" N GLU A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.546A pdb=" N VAL A 351 " --> pdb=" O TRP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'B' and resid 14 through 31 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.526A pdb=" N GLY B 138 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'C' and resid 6 through 15 Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 129 through 135 removed outlier: 4.636A pdb=" N GLN C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 149 removed outlier: 3.729A pdb=" N ARG C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.702A pdb=" N GLY D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 42 removed outlier: 3.528A pdb=" N GLU D 41 " --> pdb=" O PRO D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'E' and resid 32 through 38 removed outlier: 3.638A pdb=" N THR E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 84 Processing helix chain 'E' and resid 96 through 111 removed outlier: 4.366A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.638A pdb=" N ASP A 50 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TRP A 34 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TRP A 94 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N THR A 148 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 116 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LYS A 150 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 118 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 231 through 243 removed outlier: 5.048A pdb=" N VAL A 224 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLN A 237 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N TYR A 222 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N ARG A 239 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N LEU A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.496A pdb=" N THR B 68 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 83 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE B 87 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 9 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N TRP B 89 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 14.166A pdb=" N VAL B 7 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 18.510A pdb=" N LYS B 91 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 21.069A pdb=" N TRP B 5 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 64 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 120 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.496A pdb=" N THR B 68 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N SER B 95 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE C 102 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.552A pdb=" N ILE D 14 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 7 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 16 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE D 4 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL D 75 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET D 6 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.156A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1269 1.32 - 1.44: 2297 1.44 - 1.57: 4153 1.57 - 1.69: 15 1.69 - 1.81: 68 Bond restraints: 7802 Sorted by residual: bond pdb=" CA ASP A 130 " pdb=" C ASP A 130 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.29e-02 6.01e+03 1.86e+01 bond pdb=" N ASP A 130 " pdb=" CA ASP A 130 " ideal model delta sigma weight residual 1.459 1.417 0.042 1.23e-02 6.61e+03 1.18e+01 bond pdb=" N THR B 20 " pdb=" CA THR B 20 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.23e-02 6.61e+03 9.58e+00 bond pdb=" N ASP A 264 " pdb=" CA ASP A 264 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.23e-02 6.61e+03 9.48e+00 bond pdb=" C THR B 20 " pdb=" O THR B 20 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.19e-02 7.06e+03 9.41e+00 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 10339 2.12 - 4.24: 211 4.24 - 6.37: 29 6.37 - 8.49: 8 8.49 - 10.61: 1 Bond angle restraints: 10588 Sorted by residual: angle pdb=" N GLU C 152 " pdb=" CA GLU C 152 " pdb=" C GLU C 152 " ideal model delta sigma weight residual 110.24 120.85 -10.61 1.41e+00 5.03e-01 5.66e+01 angle pdb=" N TRP A 77 " pdb=" CA TRP A 77 " pdb=" C TRP A 77 " ideal model delta sigma weight residual 111.82 103.74 8.08 1.16e+00 7.43e-01 4.85e+01 angle pdb=" N GLY C 31 " pdb=" CA GLY C 31 " pdb=" C GLY C 31 " ideal model delta sigma weight residual 111.36 119.40 -8.04 1.17e+00 7.31e-01 4.72e+01 angle pdb=" N ASP C 34 " pdb=" CA ASP C 34 " pdb=" C ASP C 34 " ideal model delta sigma weight residual 111.33 119.34 -8.01 1.21e+00 6.83e-01 4.38e+01 angle pdb=" N GLY A 255 " pdb=" CA GLY A 255 " pdb=" C GLY A 255 " ideal model delta sigma weight residual 111.93 119.48 -7.55 1.15e+00 7.56e-01 4.31e+01 ... (remaining 10583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 4133 17.45 - 34.89: 372 34.89 - 52.34: 72 52.34 - 69.78: 24 69.78 - 87.23: 16 Dihedral angle restraints: 4617 sinusoidal: 2005 harmonic: 2612 Sorted by residual: dihedral pdb=" C4' A K 1 " pdb=" C3' A K 1 " pdb=" C2' A K 1 " pdb=" C1' A K 1 " ideal model delta sinusoidal sigma weight residual 36.34 -37.31 73.66 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' A K 4 " pdb=" C3' A K 4 " pdb=" C2' A K 4 " pdb=" C1' A K 4 " ideal model delta sinusoidal sigma weight residual 36.35 -36.46 72.80 1 3.10e+00 1.04e-01 7.04e+02 dihedral pdb=" C4' A K 5 " pdb=" C3' A K 5 " pdb=" C2' A K 5 " pdb=" C1' A K 5 " ideal model delta sinusoidal sigma weight residual 36.34 -34.27 70.61 1 3.10e+00 1.04e-01 6.67e+02 ... (remaining 4614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 915 0.059 - 0.118: 135 0.118 - 0.177: 27 0.177 - 0.236: 11 0.236 - 0.295: 8 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CA HIS A 81 " pdb=" N HIS A 81 " pdb=" C HIS A 81 " pdb=" CB HIS A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C2' A K 4 " pdb=" C3' A K 4 " pdb=" O2' A K 4 " pdb=" C1' A K 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C2' A K 1 " pdb=" C3' A K 1 " pdb=" O2' A K 1 " pdb=" C1' A K 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1093 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 82 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY B 82 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY B 82 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN B 83 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 73 " -0.012 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C HIS B 73 " 0.045 2.00e-02 2.50e+03 pdb=" O HIS B 73 " -0.017 2.00e-02 2.50e+03 pdb=" N THR B 74 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 65 " 0.032 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO E 66 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " 0.027 5.00e-02 4.00e+02 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1812 2.80 - 3.32: 6846 3.32 - 3.85: 12243 3.85 - 4.37: 14869 4.37 - 4.90: 24860 Nonbonded interactions: 60630 Sorted by model distance: nonbonded pdb=" NH2 ARG D 37 " pdb=" O ARG D 80 " model vdw 2.270 3.120 nonbonded pdb=" N GLU E 12 " pdb=" OE1 GLU E 12 " model vdw 2.278 3.120 nonbonded pdb=" O ARG D 9 " pdb=" OG1 THR D 12 " model vdw 2.349 3.040 nonbonded pdb=" N GLU A 259 " pdb=" OE1 GLU A 259 " model vdw 2.371 3.120 nonbonded pdb=" O ASN B 3 " pdb=" NH2 ARG C 83 " model vdw 2.393 3.120 ... (remaining 60625 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.006 0.056 7812 Z= 0.293 Angle : 0.724 10.611 10590 Z= 0.431 Chirality : 0.054 0.295 1096 Planarity : 0.005 0.060 1334 Dihedral : 14.988 87.231 2925 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.97 (0.29), residues: 875 helix: 1.67 (0.30), residues: 307 sheet: 1.01 (0.41), residues: 166 loop : -0.29 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 63 TYR 0.018 0.002 TYR B 111 PHE 0.015 0.002 PHE A 70 TRP 0.011 0.002 TRP A 94 HIS 0.007 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.29 ( 7802) covalent geometry : angle 0.72325 / 0.43 (10588) hydrogen bonds : bond 0.11600 / 7.25 ( 328) hydrogen bonds : angle 5.17135 / 3.63 ( 969) metal coordination : bond 0.00774 / 0.47 ( 10) metal coordination : angle 1.56574 / 0.83 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8067 (mtmt) REVERT: E 74 CYS cc_start: 0.8814 (m) cc_final: 0.8454 (m) outliers start: 0 outliers final: 1 residues processed: 143 average time/residue: 0.5725 time to fit residues: 86.1006 Evaluate side-chains 106 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 228 HIS A 229 ASN B 3 ASN C 41 GLN E 27 HIS E 68 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.094352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061396 restraints weight = 18760.769| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.07 r_work: 0.2866 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7812 Z= 0.217 Angle : 0.733 10.539 10590 Z= 0.368 Chirality : 0.058 0.866 1096 Planarity : 0.005 0.052 1334 Dihedral : 9.066 140.719 1089 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.51 % Allowed : 9.27 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.08 (0.29), residues: 875 helix: 1.88 (0.30), residues: 311 sheet: 1.28 (0.41), residues: 159 loop : -0.42 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 80 TYR 0.017 0.002 TYR B 111 PHE 0.015 0.001 PHE D 25 TRP 0.015 0.001 TRP A 94 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 ( 7802) covalent geometry : angle 0.73268 / 0.37 (10588) hydrogen bonds : bond 0.04157 / 2.68 ( 328) hydrogen bonds : angle 4.59070 / 3.18 ( 969) metal coordination : bond 0.01062 / 0.70 ( 10) metal coordination : angle 1.66822 / 0.88 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7312 (mtpt) REVERT: C 116 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8761 (mt) REVERT: D 8 ARG cc_start: 0.6917 (mtp85) cc_final: 0.6622 (mtp180) REVERT: E 33 ARG cc_start: 0.7366 (mtp85) cc_final: 0.6739 (ttp-170) outliers start: 20 outliers final: 7 residues processed: 113 average time/residue: 0.5407 time to fit residues: 64.4833 Evaluate side-chains 103 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.094599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061253 restraints weight = 18917.720| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.12 r_work: 0.2875 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7812 Z= 0.175 Angle : 0.684 11.743 10590 Z= 0.345 Chirality : 0.051 0.626 1096 Planarity : 0.004 0.051 1334 Dihedral : 9.071 140.081 1086 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.88 % Allowed : 10.78 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.22 (0.29), residues: 875 helix: 2.03 (0.31), residues: 311 sheet: 1.15 (0.41), residues: 164 loop : -0.30 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 80 TYR 0.016 0.001 TYR E 83 PHE 0.011 0.001 PHE B 112 TRP 0.013 0.001 TRP A 211 HIS 0.003 0.001 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 ( 7802) covalent geometry : angle 0.68351 / 0.34 (10588) hydrogen bonds : bond 0.03634 / 2.35 ( 328) hydrogen bonds : angle 4.35915 / 3.01 ( 969) metal coordination : bond 0.01117 / 0.72 ( 10) metal coordination : angle 1.47894 / 0.79 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 HIS cc_start: 0.8612 (t70) cc_final: 0.7931 (t-170) REVERT: B 14 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7827 (p0) REVERT: B 122 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7826 (mmmm) REVERT: C 20 LYS cc_start: 0.7811 (tppt) cc_final: 0.7542 (tptp) REVERT: C 116 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8815 (mt) REVERT: D 8 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6962 (mtp180) REVERT: D 26 GLU cc_start: 0.9566 (mt-10) cc_final: 0.9359 (pt0) REVERT: E 20 LYS cc_start: 0.7725 (tttp) cc_final: 0.7505 (tptm) REVERT: E 33 ARG cc_start: 0.7312 (mtp85) cc_final: 0.6597 (ttp-170) outliers start: 23 outliers final: 9 residues processed: 112 average time/residue: 0.5770 time to fit residues: 68.0734 Evaluate side-chains 108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS B 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.094077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061182 restraints weight = 19043.462| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.06 r_work: 0.2867 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7812 Z= 0.191 Angle : 0.681 10.809 10590 Z= 0.342 Chirality : 0.050 0.565 1096 Planarity : 0.004 0.053 1334 Dihedral : 9.012 140.745 1086 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.76 % Allowed : 12.66 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.28 (0.29), residues: 875 helix: 2.09 (0.31), residues: 310 sheet: 1.11 (0.40), residues: 164 loop : -0.22 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 80 TYR 0.016 0.001 TYR B 111 PHE 0.016 0.001 PHE D 25 TRP 0.014 0.001 TRP A 211 HIS 0.003 0.001 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 7802) covalent geometry : angle 0.68067 / 0.34 (10588) hydrogen bonds : bond 0.03527 / 2.29 ( 328) hydrogen bonds : angle 4.30505 / 2.96 ( 969) metal coordination : bond 0.00954 / 0.63 ( 10) metal coordination : angle 1.84381 / 1.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8157 (pmm150) cc_final: 0.7879 (pmm150) REVERT: B 14 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7852 (p0) REVERT: B 122 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7860 (mmmm) REVERT: C 116 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8847 (mt) REVERT: D 8 ARG cc_start: 0.7474 (mtp85) cc_final: 0.7209 (mtp180) REVERT: E 20 LYS cc_start: 0.7907 (tttp) cc_final: 0.7621 (tptm) outliers start: 22 outliers final: 12 residues processed: 107 average time/residue: 0.5623 time to fit residues: 63.5424 Evaluate side-chains 107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 0.0570 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.094854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061740 restraints weight = 18906.523| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.09 r_work: 0.2897 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7812 Z= 0.126 Angle : 0.640 11.945 10590 Z= 0.321 Chirality : 0.047 0.436 1096 Planarity : 0.004 0.044 1334 Dihedral : 8.893 141.761 1086 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.63 % Allowed : 13.91 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.40 (0.29), residues: 875 helix: 2.18 (0.31), residues: 308 sheet: 0.86 (0.38), residues: 182 loop : -0.00 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 29 TYR 0.014 0.001 TYR B 111 PHE 0.007 0.001 PHE C 32 TRP 0.014 0.001 TRP A 211 HIS 0.002 0.000 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 7802) covalent geometry : angle 0.63884 / 0.32 (10588) hydrogen bonds : bond 0.03142 / 2.03 ( 328) hydrogen bonds : angle 4.14923 / 2.85 ( 969) metal coordination : bond 0.00624 / 0.41 ( 10) metal coordination : angle 2.34414 / 1.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7683 (p0) REVERT: B 122 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7738 (mmmm) REVERT: C 116 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8856 (mt) REVERT: D 5 LEU cc_start: 0.8908 (pt) cc_final: 0.8637 (tm) REVERT: D 29 ARG cc_start: 0.7370 (ttp80) cc_final: 0.7069 (tmm160) REVERT: D 68 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8550 (mtm-85) REVERT: E 104 LEU cc_start: 0.9145 (tt) cc_final: 0.8940 (tp) outliers start: 21 outliers final: 9 residues processed: 106 average time/residue: 0.5365 time to fit residues: 60.0210 Evaluate side-chains 101 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.0470 chunk 12 optimal weight: 0.0060 chunk 2 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062068 restraints weight = 18952.013| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.13 r_work: 0.2910 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7812 Z= 0.125 Angle : 0.643 12.695 10590 Z= 0.321 Chirality : 0.047 0.377 1096 Planarity : 0.004 0.045 1334 Dihedral : 8.806 141.649 1086 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.88 % Allowed : 14.66 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.46 (0.29), residues: 875 helix: 2.20 (0.31), residues: 308 sheet: 0.83 (0.38), residues: 183 loop : 0.09 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 29 TYR 0.035 0.001 TYR E 18 PHE 0.013 0.001 PHE D 25 TRP 0.013 0.001 TRP A 211 HIS 0.002 0.001 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 7802) covalent geometry : angle 0.64296 / 0.32 (10588) hydrogen bonds : bond 0.03046 / 1.97 ( 328) hydrogen bonds : angle 4.05960 / 2.78 ( 969) metal coordination : bond 0.00587 / 0.39 ( 10) metal coordination : angle 1.83276 / 0.98 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8212 (pmm150) cc_final: 0.7938 (pmm150) REVERT: A 237 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: B 14 ASP cc_start: 0.8021 (p0) cc_final: 0.7636 (p0) REVERT: B 122 LYS cc_start: 0.8047 (mmtm) cc_final: 0.7686 (mmpt) REVERT: C 116 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8949 (mp) REVERT: D 5 LEU cc_start: 0.8933 (pt) cc_final: 0.8694 (tm) REVERT: E 20 LYS cc_start: 0.7891 (tptm) cc_final: 0.7653 (tptp) REVERT: E 29 PHE cc_start: 0.7667 (m-80) cc_final: 0.7292 (m-80) outliers start: 23 outliers final: 10 residues processed: 110 average time/residue: 0.5144 time to fit residues: 59.9718 Evaluate side-chains 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.0060 chunk 57 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 69 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.095716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.063455 restraints weight = 18936.351| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.04 r_work: 0.2924 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7812 Z= 0.120 Angle : 0.659 14.148 10590 Z= 0.325 Chirality : 0.046 0.332 1096 Planarity : 0.004 0.045 1334 Dihedral : 8.731 141.339 1086 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.26 % Allowed : 15.91 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.51 (0.29), residues: 875 helix: 2.22 (0.31), residues: 308 sheet: 0.86 (0.39), residues: 180 loop : 0.15 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 68 TYR 0.032 0.001 TYR E 18 PHE 0.011 0.001 PHE C 32 TRP 0.015 0.001 TRP A 211 HIS 0.002 0.000 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7802) covalent geometry : angle 0.65846 / 0.33 (10588) hydrogen bonds : bond 0.02954 / 1.90 ( 328) hydrogen bonds : angle 4.03768 / 2.76 ( 969) metal coordination : bond 0.00505 / 0.33 ( 10) metal coordination : angle 2.00486 / 1.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.8918 (ttt) REVERT: A 237 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8548 (pm20) REVERT: B 14 ASP cc_start: 0.7974 (p0) cc_final: 0.7593 (p0) REVERT: C 116 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8966 (mp) REVERT: D 5 LEU cc_start: 0.8898 (pt) cc_final: 0.8682 (tm) REVERT: D 28 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8148 (tppt) REVERT: E 29 PHE cc_start: 0.7538 (m-80) cc_final: 0.7211 (m-80) outliers start: 18 outliers final: 7 residues processed: 102 average time/residue: 0.5529 time to fit residues: 59.5935 Evaluate side-chains 97 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 0.0470 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.095463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062638 restraints weight = 19041.808| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.10 r_work: 0.2919 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7812 Z= 0.134 Angle : 0.682 14.303 10590 Z= 0.336 Chirality : 0.046 0.319 1096 Planarity : 0.004 0.046 1334 Dihedral : 8.707 141.097 1086 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.88 % Allowed : 17.29 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.44 (0.29), residues: 875 helix: 2.10 (0.31), residues: 314 sheet: 0.76 (0.39), residues: 182 loop : 0.16 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 213 TYR 0.030 0.001 TYR E 18 PHE 0.012 0.001 PHE B 112 TRP 0.016 0.001 TRP A 211 HIS 0.003 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7802) covalent geometry : angle 0.68198 / 0.34 (10588) hydrogen bonds : bond 0.03027 / 1.96 ( 328) hydrogen bonds : angle 4.04967 / 2.77 ( 969) metal coordination : bond 0.00926 / 0.57 ( 10) metal coordination : angle 1.32831 / 0.71 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8943 (ttt) REVERT: A 213 ARG cc_start: 0.8218 (pmm150) cc_final: 0.7771 (pmm150) REVERT: A 237 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8552 (pm20) REVERT: B 14 ASP cc_start: 0.8003 (p0) cc_final: 0.7622 (p0) REVERT: B 122 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7525 (mmpt) REVERT: C 116 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8950 (mp) REVERT: D 28 LYS cc_start: 0.8660 (mmmm) cc_final: 0.7990 (tppt) REVERT: E 29 PHE cc_start: 0.7458 (m-80) cc_final: 0.7200 (m-80) REVERT: E 45 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6192 (ppp) REVERT: E 105 MET cc_start: 0.9102 (ptp) cc_final: 0.8611 (mpp) outliers start: 15 outliers final: 6 residues processed: 102 average time/residue: 0.5574 time to fit residues: 59.9365 Evaluate side-chains 99 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 45 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 GLN ** 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 = 0.3817 r_free = 0.3817 target = 0.094832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062064 restraints weight = 19162.994| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.09 r_work: 0.2913 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7812 Z= 0.154 Angle : 0.707 14.501 10590 Z= 0.347 Chirality : 0.047 0.334 1096 Planarity : 0.004 0.053 1334 Dihedral : 8.720 141.279 1086 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.38 % Allowed : 18.05 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.42 (0.29), residues: 875 helix: 2.15 (0.31), residues: 314 sheet: 0.71 (0.39), residues: 177 loop : 0.11 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 169 TYR 0.040 0.001 TYR E 18 PHE 0.011 0.001 PHE B 112 TRP 0.018 0.001 TRP A 211 HIS 0.003 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 7802) covalent geometry : angle 0.70672 / 0.35 (10588) hydrogen bonds : bond 0.03143 / 2.03 ( 328) hydrogen bonds : angle 4.09195 / 2.80 ( 969) metal coordination : bond 0.00759 / 0.50 ( 10) metal coordination : angle 1.50481 / 0.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.8967 (ttt) REVERT: A 237 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: B 14 ASP cc_start: 0.8059 (p0) cc_final: 0.7653 (p0) REVERT: B 122 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7555 (mmpt) REVERT: C 116 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8951 (mp) REVERT: D 7 ILE cc_start: 0.9230 (mp) cc_final: 0.8971 (mm) REVERT: E 29 PHE cc_start: 0.7453 (m-80) cc_final: 0.7177 (m-80) REVERT: E 45 MET cc_start: 0.6879 (tmm) cc_final: 0.6497 (ppp) REVERT: E 105 MET cc_start: 0.9032 (ptp) cc_final: 0.8548 (mpp) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.5287 time to fit residues: 53.6596 Evaluate side-chains 96 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 GLN ** 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 = 0.3805 r_free = 0.3805 target = 0.094013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061259 restraints weight = 19073.799| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.06 r_work: 0.2889 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7812 Z= 0.201 Angle : 0.745 14.752 10590 Z= 0.366 Chirality : 0.049 0.394 1096 Planarity : 0.004 0.047 1334 Dihedral : 8.810 142.159 1086 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.01 % Allowed : 17.79 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.38 (0.29), residues: 875 helix: 2.11 (0.31), residues: 315 sheet: 0.87 (0.40), residues: 171 loop : -0.00 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.047 0.002 TYR E 18 PHE 0.013 0.001 PHE B 112 TRP 0.016 0.001 TRP A 211 HIS 0.004 0.001 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 ( 7802) covalent geometry : angle 0.74504 / 0.37 (10588) hydrogen bonds : bond 0.03454 / 2.23 ( 328) hydrogen bonds : angle 4.15851 / 2.86 ( 969) metal coordination : bond 0.01003 / 0.66 ( 10) metal coordination : angle 1.42310 / 0.77 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7619 (mmp80) REVERT: A 149 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.8954 (ttt) REVERT: B 14 ASP cc_start: 0.8150 (p0) cc_final: 0.7722 (p0) REVERT: B 122 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7575 (mmpt) REVERT: C 116 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8941 (mp) REVERT: E 29 PHE cc_start: 0.7476 (m-80) cc_final: 0.7137 (m-80) REVERT: E 45 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6632 (ppp) REVERT: E 105 MET cc_start: 0.9025 (ptp) cc_final: 0.8549 (mpp) outliers start: 16 outliers final: 7 residues processed: 97 average time/residue: 0.5425 time to fit residues: 55.5664 Evaluate side-chains 96 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 0.0970 chunk 7 optimal weight: 0.0030 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.095138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062538 restraints weight = 18997.826| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.07 r_work: 0.2920 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7812 Z= 0.132 Angle : 0.723 15.233 10590 Z= 0.353 Chirality : 0.048 0.303 1096 Planarity : 0.006 0.183 1334 Dihedral : 8.778 142.165 1086 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.75 % Allowed : 18.05 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.43 (0.29), residues: 875 helix: 2.07 (0.31), residues: 314 sheet: 0.75 (0.39), residues: 177 loop : 0.18 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 29 TYR 0.048 0.001 TYR E 18 PHE 0.011 0.001 PHE C 32 TRP 0.022 0.001 TRP A 211 HIS 0.003 0.000 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 7802) covalent geometry : angle 0.72298 / 0.35 (10588) hydrogen bonds : bond 0.03078 / 1.98 ( 328) hydrogen bonds : angle 4.12512 / 2.83 ( 969) metal coordination : bond 0.00694 / 0.44 ( 10) metal coordination : angle 1.79186 / 0.96 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.80 seconds wall clock time: 44 minutes 52.87 seconds (2692.87 seconds total)