Starting phenix.real_space_refine on Tue Mar 3 17:36:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cx0_27032/03_2026/8cx0_27032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx0_27032/03_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_27032/03_2026/8cx0_27032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx0_27032/03_2026/8cx0_27032.map" model { file = "/net/cci-nas-00/data/ceres_data/8cx0_27032/03_2026/8cx0_27032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx0_27032/03_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-dev-5986/lib/python3.9/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: {'RNA': 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: 1.78, per 1000 atoms: 0.23 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: 0.90 Conformation dependent library (CDL) restraints added in 269.3 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: 0.25 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: 0.95 Time building geometry restraints manager: 1.13 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: 10369 2.12 - 4.24: 186 4.24 - 6.37: 24 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: 4159 17.45 - 34.89: 362 34.89 - 52.34: 71 52.34 - 69.78: 12 69.78 - 87.23: 13 Dihedral angle restraints: 4617 sinusoidal: 2005 harmonic: 2612 Sorted by residual: dihedral pdb=" CA PHE C 17 " pdb=" C PHE C 17 " pdb=" N PHE C 18 " pdb=" CA PHE C 18 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA GLU C 16 " pdb=" C GLU C 16 " pdb=" N PHE C 17 " pdb=" CA PHE C 17 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA TYR B 110 " pdb=" C TYR B 110 " pdb=" N TYR B 111 " pdb=" CA TYR B 111 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 4614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 931 0.059 - 0.118: 133 0.118 - 0.177: 27 0.177 - 0.236: 4 0.236 - 0.295: 1 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=" CA ARG A 29 " pdb=" N ARG A 29 " pdb=" C ARG A 29 " pdb=" CB ARG A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' A K 3 " pdb=" C4' A K 3 " pdb=" O3' A K 3 " pdb=" C2' A K 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.13e+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: 4.170 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.690 Find NCS groups from input model: 0.020 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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= 0.292 Angle : 0.699 10.611 10590 Z= 0.425 Chirality : 0.047 0.295 1096 Planarity : 0.005 0.060 1334 Dihedral : 14.184 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 covalent geometry : bond 0.00557 ( 7802) covalent geometry : angle 0.69880 (10588) hydrogen bonds : bond 0.11600 ( 328) hydrogen bonds : angle 5.17135 ( 969) metal coordination : bond 0.00774 ( 10) metal coordination : angle 1.56574 ( 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 : 0.297 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: 0.6286 time to fit residues: 94.4150 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 : 0.239 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 229 ASN B 3 ASN B 27 HIS C 41 GLN E 27 HIS E 68 HIS E 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.093909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060406 restraints weight = 18816.478| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.10 r_work: 0.2843 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7812 Z= 0.213 Angle : 0.658 9.566 10590 Z= 0.343 Chirality : 0.045 0.204 1096 Planarity : 0.005 0.049 1334 Dihedral : 6.620 59.393 1089 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.38 % Allowed : 9.65 % Favored : 87.97 % 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: 1.09 (0.29), residues: 875 helix: 1.88 (0.31), 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 0.009 0.001 ARG D 9 TYR 0.018 0.002 TYR E 83 PHE 0.014 0.002 PHE D 25 TRP 0.016 0.001 TRP A 94 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 7802) covalent geometry : angle 0.65795 (10588) hydrogen bonds : bond 0.04090 ( 328) hydrogen bonds : angle 4.58733 ( 969) metal coordination : bond 0.01217 ( 10) metal coordination : angle 1.58770 ( 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 126 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7360 (mtpt) REVERT: C 116 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8784 (mt) REVERT: D 8 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6676 (mtp180) REVERT: E 20 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7506 (tptp) REVERT: E 33 ARG cc_start: 0.7375 (mtp85) cc_final: 0.6771 (ttp-170) outliers start: 19 outliers final: 7 residues processed: 111 average time/residue: 0.6610 time to fit residues: 77.1976 Evaluate side-chains 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.094492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.061145 restraints weight = 18909.506| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.11 r_work: 0.2865 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7812 Z= 0.151 Angle : 0.623 11.661 10590 Z= 0.322 Chirality : 0.042 0.178 1096 Planarity : 0.004 0.057 1334 Dihedral : 6.482 58.497 1086 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.88 % Allowed : 10.90 % Favored : 86.22 % 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: 1.24 (0.29), residues: 875 helix: 2.05 (0.31), residues: 311 sheet: 1.04 (0.40), residues: 167 loop : -0.23 (0.31), residues: 397 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 0.010 0.001 PHE B 112 TRP 0.012 0.001 TRP A 211 HIS 0.003 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7802) covalent geometry : angle 0.62321 (10588) hydrogen bonds : bond 0.03476 ( 328) hydrogen bonds : angle 4.33034 ( 969) metal coordination : bond 0.01085 ( 10) metal coordination : angle 1.49223 ( 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 125 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7792 (p0) REVERT: B 122 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7804 (mmmm) REVERT: C 20 LYS cc_start: 0.7874 (tppt) cc_final: 0.7599 (tptp) REVERT: C 116 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8833 (mt) REVERT: D 8 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6993 (mtp180) REVERT: D 26 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9364 (pt0) REVERT: E 33 ARG cc_start: 0.7328 (mtp85) cc_final: 0.6616 (ttp-170) outliers start: 23 outliers final: 9 residues processed: 111 average time/residue: 0.6042 time to fit residues: 70.7133 Evaluate side-chains 107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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: 0.5980 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.093464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.060256 restraints weight = 19154.766| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.09 r_work: 0.2848 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7812 Z= 0.196 Angle : 0.628 10.960 10590 Z= 0.322 Chirality : 0.043 0.156 1096 Planarity : 0.004 0.053 1334 Dihedral : 6.426 56.484 1086 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.88 % Allowed : 12.53 % 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: 1.27 (0.29), residues: 875 helix: 2.03 (0.30), residues: 310 sheet: 1.08 (0.40), residues: 164 loop : -0.17 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 80 TYR 0.017 0.001 TYR B 111 PHE 0.014 0.001 PHE D 25 TRP 0.014 0.001 TRP A 211 HIS 0.004 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7802) covalent geometry : angle 0.62750 (10588) hydrogen bonds : bond 0.03570 ( 328) hydrogen bonds : angle 4.29209 ( 969) metal coordination : bond 0.00968 ( 10) metal coordination : angle 1.92207 ( 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 120 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7853 (p0) REVERT: B 122 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7897 (mmmm) REVERT: C 116 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8856 (mt) REVERT: D 8 ARG cc_start: 0.7495 (mtp85) cc_final: 0.7250 (mtp180) outliers start: 23 outliers final: 12 residues processed: 107 average time/residue: 0.5788 time to fit residues: 65.4152 Evaluate side-chains 105 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 21 LEU 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: 0.8980 chunk 74 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.093358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060052 restraints weight = 19038.555| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.09 r_work: 0.2848 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7812 Z= 0.183 Angle : 0.621 12.126 10590 Z= 0.317 Chirality : 0.042 0.152 1096 Planarity : 0.004 0.049 1334 Dihedral : 6.410 56.331 1086 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.76 % Allowed : 14.04 % Favored : 83.21 % 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: 1.35 (0.29), residues: 875 helix: 2.14 (0.31), residues: 309 sheet: 1.05 (0.40), residues: 164 loop : -0.11 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.016 0.001 TYR B 111 PHE 0.010 0.001 PHE B 112 TRP 0.014 0.001 TRP A 211 HIS 0.003 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7802) covalent geometry : angle 0.62024 (10588) hydrogen bonds : bond 0.03482 ( 328) hydrogen bonds : angle 4.21107 ( 969) metal coordination : bond 0.00926 ( 10) metal coordination : angle 1.87535 ( 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 117 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8221 (pmm150) cc_final: 0.7952 (pmm150) REVERT: B 14 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7834 (p0) REVERT: B 122 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7842 (mmmm) REVERT: C 116 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8933 (mp) REVERT: D 5 LEU cc_start: 0.8886 (pt) cc_final: 0.8629 (tm) outliers start: 22 outliers final: 14 residues processed: 107 average time/residue: 0.5562 time to fit residues: 62.9770 Evaluate side-chains 106 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 153 LEU 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 D residue 64 SER Chi-restraints excluded: chain E residue 21 LEU 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: 5.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 26 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.093586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060429 restraints weight = 18993.938| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.09 r_work: 0.2859 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2771 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= 0.148 Angle : 0.614 12.725 10590 Z= 0.311 Chirality : 0.042 0.152 1096 Planarity : 0.004 0.063 1334 Dihedral : 6.352 56.108 1086 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.76 % Allowed : 14.16 % Favored : 83.08 % 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: 1.36 (0.29), residues: 875 helix: 2.18 (0.31), residues: 309 sheet: 0.81 (0.39), residues: 179 loop : -0.04 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 80 TYR 0.032 0.001 TYR E 18 PHE 0.012 0.001 PHE D 25 TRP 0.015 0.001 TRP A 211 HIS 0.003 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7802) covalent geometry : angle 0.61289 (10588) hydrogen bonds : bond 0.03269 ( 328) hydrogen bonds : angle 4.12837 ( 969) metal coordination : bond 0.00751 ( 10) metal coordination : angle 2.36732 ( 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 117 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7773 (p0) REVERT: B 122 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7784 (mmmm) REVERT: C 116 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8937 (mp) REVERT: D 5 LEU cc_start: 0.8908 (pt) cc_final: 0.8602 (tm) REVERT: D 68 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8318 (mtm-85) REVERT: E 45 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5873 (ppp) outliers start: 22 outliers final: 11 residues processed: 108 average time/residue: 0.5558 time to fit residues: 63.4968 Evaluate side-chains 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 120 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 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 21 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3795 r_free = 0.3795 target = 0.093912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060887 restraints weight = 19124.284| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.11 r_work: 0.2871 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2907 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= 0.134 Angle : 0.625 14.095 10590 Z= 0.317 Chirality : 0.042 0.182 1096 Planarity : 0.004 0.051 1334 Dihedral : 6.302 55.613 1086 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.01 % Allowed : 14.41 % Favored : 82.58 % 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: 1.33 (0.29), residues: 875 helix: 2.08 (0.31), residues: 314 sheet: 0.81 (0.39), residues: 179 loop : -0.04 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 29 TYR 0.032 0.001 TYR E 18 PHE 0.008 0.001 PHE B 112 TRP 0.013 0.001 TRP A 211 HIS 0.002 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7802) covalent geometry : angle 0.62392 (10588) hydrogen bonds : bond 0.03184 ( 328) hydrogen bonds : angle 4.11773 ( 969) metal coordination : bond 0.00631 ( 10) metal coordination : angle 2.42467 ( 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 117 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8167 (pmm150) cc_final: 0.7808 (pmm150) REVERT: B 14 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7634 (p0) REVERT: C 116 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8950 (mp) REVERT: D 5 LEU cc_start: 0.8878 (pt) cc_final: 0.8622 (tm) REVERT: E 29 PHE cc_start: 0.7627 (m-80) cc_final: 0.7227 (m-80) REVERT: E 105 MET cc_start: 0.9071 (ptp) cc_final: 0.8557 (mpp) outliers start: 24 outliers final: 11 residues processed: 107 average time/residue: 0.5468 time to fit residues: 61.9544 Evaluate side-chains 102 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 120 ILE Chi-restraints excluded: chain B residue 130 SER 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 7 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 21 LEU 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: 7.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 chunk 4 optimal weight: 0.3980 chunk 32 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3807 r_free = 0.3807 target = 0.094513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061611 restraints weight = 19043.722| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.07 r_work: 0.2890 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7812 Z= 0.120 Angle : 0.640 14.269 10590 Z= 0.321 Chirality : 0.042 0.200 1096 Planarity : 0.004 0.047 1334 Dihedral : 6.222 54.132 1086 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.13 % Allowed : 16.29 % Favored : 81.58 % 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: 1.34 (0.29), residues: 875 helix: 2.05 (0.31), residues: 314 sheet: 0.74 (0.39), residues: 180 loop : 0.06 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 80 TYR 0.033 0.001 TYR E 18 PHE 0.012 0.001 PHE C 32 TRP 0.017 0.001 TRP A 211 HIS 0.002 0.000 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7802) covalent geometry : angle 0.63963 (10588) hydrogen bonds : bond 0.03020 ( 328) hydrogen bonds : angle 4.07620 ( 969) metal coordination : bond 0.00531 ( 10) metal coordination : angle 2.45793 ( 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 109 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.8941 (ttt) REVERT: A 237 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: B 14 ASP cc_start: 0.7960 (p0) cc_final: 0.7582 (p0) REVERT: C 116 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8952 (mp) REVERT: D 5 LEU cc_start: 0.8905 (pt) cc_final: 0.8589 (tm) REVERT: D 28 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8111 (tppt) REVERT: D 68 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8408 (mtm-85) outliers start: 17 outliers final: 7 residues processed: 102 average time/residue: 0.5715 time to fit residues: 61.6166 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 : 0.288 ------------------------------------------------------------------------------- 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 130 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 37 LEU 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: 1.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3789 r_free = 0.3789 target = 0.093401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.060346 restraints weight = 19225.801| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.09 r_work: 0.2863 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7812 Z= 0.171 Angle : 0.663 14.408 10590 Z= 0.333 Chirality : 0.043 0.220 1096 Planarity : 0.004 0.044 1334 Dihedral : 6.295 55.437 1086 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.63 % Allowed : 16.67 % Favored : 81.70 % 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: 1.31 (0.29), residues: 875 helix: 2.07 (0.31), residues: 314 sheet: 0.78 (0.39), residues: 178 loop : -0.03 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 80 TYR 0.036 0.001 TYR E 18 PHE 0.012 0.001 PHE C 32 TRP 0.017 0.001 TRP A 211 HIS 0.004 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7802) covalent geometry : angle 0.66235 (10588) hydrogen bonds : bond 0.03298 ( 328) hydrogen bonds : angle 4.18076 ( 969) metal coordination : bond 0.00769 ( 10) metal coordination : angle 2.66257 ( 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 106 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.8995 (ttt) REVERT: A 228 HIS cc_start: 0.8686 (t70) cc_final: 0.8003 (t-170) REVERT: B 14 ASP cc_start: 0.8079 (p0) cc_final: 0.7648 (p0) REVERT: C 116 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8948 (mp) REVERT: D 7 ILE cc_start: 0.9091 (mp) cc_final: 0.8859 (mm) REVERT: D 28 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8093 (tppt) REVERT: E 45 MET cc_start: 0.6677 (tmm) cc_final: 0.6257 (ppp) REVERT: E 105 MET cc_start: 0.8990 (ptp) cc_final: 0.8649 (mpp) outliers start: 13 outliers final: 8 residues processed: 101 average time/residue: 0.5762 time to fit residues: 61.5242 Evaluate side-chains 96 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 130 SER 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 21 LEU Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** 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 = 0.3775 r_free = 0.3775 target = 0.092613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.059327 restraints weight = 19139.099| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.08 r_work: 0.2835 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7812 Z= 0.229 Angle : 0.709 14.016 10590 Z= 0.359 Chirality : 0.044 0.244 1096 Planarity : 0.004 0.046 1334 Dihedral : 6.463 55.518 1086 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.50 % Allowed : 17.17 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.19 (0.29), residues: 875 helix: 1.98 (0.30), residues: 316 sheet: 0.80 (0.40), residues: 176 loop : -0.18 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 68 TYR 0.017 0.002 TYR B 111 PHE 0.012 0.001 PHE C 32 TRP 0.024 0.001 TRP A 211 HIS 0.012 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 7802) covalent geometry : angle 0.70814 (10588) hydrogen bonds : bond 0.03630 ( 328) hydrogen bonds : angle 4.29291 ( 969) metal coordination : bond 0.00991 ( 10) metal coordination : angle 2.73347 ( 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 105 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7626 (mmp80) REVERT: C 116 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8898 (mp) REVERT: D 5 LEU cc_start: 0.8546 (mm) cc_final: 0.7965 (tm) REVERT: D 68 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8448 (mtm-85) REVERT: E 45 MET cc_start: 0.6679 (tmm) cc_final: 0.6242 (ppp) REVERT: E 105 MET cc_start: 0.8995 (ptp) cc_final: 0.8649 (mpp) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.5489 time to fit residues: 58.8068 Evaluate side-chains 98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 130 SER 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 21 LEU Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 5.9990 chunk 7 optimal weight: 0.0020 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3795 r_free = 0.3795 target = 0.093521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.060608 restraints weight = 19023.026| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.06 r_work: 0.2868 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7812 Z= 0.138 Angle : 0.689 13.607 10590 Z= 0.345 Chirality : 0.043 0.231 1096 Planarity : 0.006 0.186 1334 Dihedral : 6.405 54.163 1086 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.00 % Allowed : 18.17 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.25 (0.29), residues: 875 helix: 2.00 (0.30), residues: 315 sheet: 0.69 (0.39), residues: 179 loop : -0.03 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 29 TYR 0.018 0.001 TYR E 83 PHE 0.012 0.001 PHE C 32 TRP 0.024 0.001 TRP A 211 HIS 0.003 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7802) covalent geometry : angle 0.68743 (10588) hydrogen bonds : bond 0.03213 ( 328) hydrogen bonds : angle 4.23044 ( 969) metal coordination : bond 0.00607 ( 10) metal coordination : angle 2.88586 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.36 seconds wall clock time: 49 minutes 37.51 seconds (2977.51 seconds total)