Starting phenix.real_space_refine on Fri Sep 11 00:14:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7j_65728/09_2026/9w7j_65728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7j_65728/09_2026/9w7j_65728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w7j_65728/09_2026/9w7j_65728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7j_65728/09_2026/9w7j_65728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w7j_65728/09_2026/9w7j_65728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7j_65728/09_2026/9w7j_65728.map" } resolution = 2.97 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= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 3587 2.51 5 N 981 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s 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: 5733 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 781 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Chain: "B" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3098 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 29, 'TRANS': 369} Chain breaks: 4 Chain: "D" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Time building chain proxies: 1.36, per 1000 atoms: 0.24 Number of scatterers: 5733 At special positions: 0 Unit cell: (73.528, 90.496, 107.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1126 8.00 N 981 7.00 C 3587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 268 " - pdb=" SG CYS C 285 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 540 " distance=2.03 Simple disulfide: pdb=" SG CYS C 488 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 489 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 504 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 240.8 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 24 sheets defined 6.2% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.840A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 removed outlier: 4.142A pdb=" N VAL C 73 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS C 75 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 664 through 673 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 99 through 104 removed outlier: 3.728A pdb=" N HIS D 104 " --> pdb=" O CYS D 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.503A pdb=" N SER A 7 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 22 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 19 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 3.603A pdb=" N ASP A 101 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 13 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.926A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 4.098A pdb=" N TYR B 109 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLU B 100 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE B 107 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.720A pdb=" N TYR C 302 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 318 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 84 Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 103 removed outlier: 8.274A pdb=" N LEU C 99 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 116 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 101 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N SER C 116 " --> pdb=" O MET C 135 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N MET C 135 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS C 131 " --> pdb=" O GLY C 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 103 removed outlier: 8.274A pdb=" N LEU C 99 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER C 116 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 101 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 11.417A pdb=" N ILE C 113 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N ARG C 169 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 11.585A pdb=" N VAL C 115 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N LEU C 167 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LEU C 117 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE C 121 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N THR C 161 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 149 through 151 removed outlier: 4.141A pdb=" N GLU C 174 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 178 " --> pdb=" O CYS C 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 217 through 221 Processing sheet with id=AB3, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 246 through 247 Processing sheet with id=AB5, first strand: chain 'C' and resid 472 through 474 removed outlier: 3.616A pdb=" N TYR C 472 " --> pdb=" O ALA C 547 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 477 through 480 Processing sheet with id=AB7, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB8, first strand: chain 'C' and resid 513 through 514 removed outlier: 3.568A pdb=" N GLY C 517 " --> pdb=" O MET C 514 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 605 through 606 Processing sheet with id=AC1, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC2, first strand: chain 'C' and resid 646 through 647 Processing sheet with id=AC3, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.794A pdb=" N VAL D 12 " --> pdb=" O SER D 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.907A pdb=" N GLY D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG D 38 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS D 33 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU D 97 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.907A pdb=" N GLY D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG D 38 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS D 33 " --> pdb=" O VAL D 98 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 501 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: 0.78 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1873 1.34 - 1.46: 1434 1.46 - 1.58: 2512 1.58 - 1.70: 1 1.70 - 1.82: 50 Bond restraints: 5870 Sorted by residual: bond pdb=" CB PRO C 658 " pdb=" CG PRO C 658 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.94e+00 bond pdb=" CB MET C 135 " pdb=" CG MET C 135 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB CYS C 285 " pdb=" SG CYS C 285 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" C GLN A 38 " pdb=" N LYS A 39 " ideal model delta sigma weight residual 1.329 1.309 0.020 1.86e-02 2.89e+03 1.12e+00 bond pdb=" CA VAL B 118 " pdb=" CB VAL B 118 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.10e+00 ... (remaining 5865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 7588 1.37 - 2.74: 305 2.74 - 4.11: 57 4.11 - 5.48: 7 5.48 - 6.86: 6 Bond angle restraints: 7963 Sorted by residual: angle pdb=" N ILE C 97 " pdb=" CA ILE C 97 " pdb=" C ILE C 97 " ideal model delta sigma weight residual 111.91 107.63 4.28 8.90e-01 1.26e+00 2.31e+01 angle pdb=" C ASN C 299 " pdb=" N TRP C 300 " pdb=" CA TRP C 300 " ideal model delta sigma weight residual 122.74 116.45 6.29 1.82e+00 3.02e-01 1.20e+01 angle pdb=" N SER C 153 " pdb=" CA SER C 153 " pdb=" C SER C 153 " ideal model delta sigma weight residual 114.56 110.22 4.34 1.27e+00 6.20e-01 1.17e+01 angle pdb=" N ALA D 91 " pdb=" CA ALA D 91 " pdb=" C ALA D 91 " ideal model delta sigma weight residual 107.73 111.76 -4.03 1.34e+00 5.57e-01 9.06e+00 angle pdb=" CA PRO C 658 " pdb=" N PRO C 658 " pdb=" CD PRO C 658 " ideal model delta sigma weight residual 112.00 107.79 4.21 1.40e+00 5.10e-01 9.05e+00 ... (remaining 7958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 3225 16.80 - 33.60: 241 33.60 - 50.41: 33 50.41 - 67.21: 11 67.21 - 84.01: 7 Dihedral angle restraints: 3517 sinusoidal: 1378 harmonic: 2139 Sorted by residual: dihedral pdb=" CB CYS C 489 " pdb=" SG CYS C 489 " pdb=" SG CYS C 522 " pdb=" CB CYS C 522 " ideal model delta sinusoidal sigma weight residual 93.00 124.72 -31.72 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CB CYS A 23 " pdb=" SG CYS A 23 " pdb=" SG CYS A 88 " pdb=" CB CYS A 88 " ideal model delta sinusoidal sigma weight residual 93.00 62.02 30.98 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA HIS C 164 " pdb=" C HIS C 164 " pdb=" N PHE C 165 " pdb=" CA PHE C 165 " ideal model delta harmonic sigma weight residual -180.00 -162.68 -17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 3514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 463 0.028 - 0.056: 259 0.056 - 0.083: 66 0.083 - 0.111: 52 0.111 - 0.139: 19 Chirality restraints: 859 Sorted by residual: chirality pdb=" CA ILE C 166 " pdb=" N ILE C 166 " pdb=" C ILE C 166 " pdb=" CB ILE C 166 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE C 102 " pdb=" N ILE C 102 " pdb=" C ILE C 102 " pdb=" CB ILE C 102 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA VAL C 150 " pdb=" N VAL C 150 " pdb=" C VAL C 150 " pdb=" CB VAL C 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 856 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 300 " 0.036 2.00e-02 2.50e+03 2.79e-02 1.95e+01 pdb=" CG TRP C 300 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP C 300 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 300 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 300 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 300 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 300 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 300 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 300 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 300 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 485 " -0.015 2.00e-02 2.50e+03 1.46e-02 4.27e+00 pdb=" CG TYR C 485 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR C 485 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 485 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 485 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 485 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 485 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 485 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 58 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 59 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " 0.020 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 234 2.71 - 3.26: 5423 3.26 - 3.81: 9259 3.81 - 4.35: 12160 4.35 - 4.90: 20824 Nonbonded interactions: 47900 Sorted by model distance: nonbonded pdb=" O ASP C 142 " pdb=" OG SER C 183 " model vdw 2.166 3.040 nonbonded pdb=" OD2 ASP C 471 " pdb=" OH TYR C 615 " model vdw 2.221 3.040 nonbonded pdb=" O TYR C 74 " pdb=" NH2 ARG C 133 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR C 643 " pdb=" OE1 GLN C 661 " model vdw 2.282 3.040 nonbonded pdb=" OG SER B 52 " pdb=" OG SER B 57 " model vdw 2.287 3.040 ... (remaining 47895 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: 3.340 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.600 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.004 0.099 5884 Z= 0.180 Angle : 0.663 6.855 7991 Z= 0.376 Chirality : 0.043 0.139 859 Planarity : 0.004 0.037 1035 Dihedral : 12.531 84.010 2115 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.65 (0.30), residues: 730 helix: -1.15 (1.15), residues: 15 sheet: -0.00 (0.33), residues: 236 loop : -0.61 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 316 TYR 0.036 0.002 TYR C 485 PHE 0.011 0.002 PHE C 521 TRP 0.076 0.003 TRP C 300 HIS 0.008 0.002 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 5870) covalent geometry : angle 0.65839 / 0.37 ( 7963) SS BOND : bond 0.00210 / 0.12 ( 14) SS BOND : angle 1.45102 / 1.02 ( 28) hydrogen bonds : bond 0.25884 / 18.00 ( 188) hydrogen bonds : angle 11.06377 / 7.51 ( 501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.190 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 100 average time/residue: 0.4067 time to fit residues: 43.2286 Evaluate side-chains 73 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 HIS ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.181052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.159113 restraints weight = 6673.981| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.79 r_work: 0.3739 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5884 Z= 0.157 Angle : 0.625 6.640 7991 Z= 0.334 Chirality : 0.045 0.150 859 Planarity : 0.005 0.038 1035 Dihedral : 4.831 19.764 812 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 8.59 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.52 (0.30), residues: 730 helix: -0.62 (1.15), residues: 15 sheet: 0.18 (0.34), residues: 235 loop : -0.59 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 673 TYR 0.013 0.001 TYR C 511 PHE 0.012 0.002 PHE D 67 TRP 0.010 0.002 TRP B 110 HIS 0.009 0.002 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 5870) covalent geometry : angle 0.62096 / 0.33 ( 7963) SS BOND : bond 0.00208 / 0.14 ( 14) SS BOND : angle 1.29717 / 0.92 ( 28) hydrogen bonds : bond 0.04563 / 3.20 ( 188) hydrogen bonds : angle 7.72281 / 5.29 ( 501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.236 Fit side-chains REVERT: C 629 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6321 (pt) REVERT: D 68 THR cc_start: 0.7931 (m) cc_final: 0.7730 (t) outliers start: 14 outliers final: 10 residues processed: 94 average time/residue: 0.3818 time to fit residues: 38.4084 Evaluate side-chains 89 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 631 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 235 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.182665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.160585 restraints weight = 6604.838| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.78 r_work: 0.3748 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5884 Z= 0.149 Angle : 0.588 6.080 7991 Z= 0.313 Chirality : 0.044 0.151 859 Planarity : 0.004 0.039 1035 Dihedral : 4.627 18.593 810 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.54 % Allowed : 14.47 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.48 (0.30), residues: 730 helix: -0.99 (1.25), residues: 15 sheet: 0.24 (0.35), residues: 229 loop : -0.56 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 133 TYR 0.013 0.001 TYR C 511 PHE 0.009 0.001 PHE C 165 TRP 0.009 0.001 TRP B 110 HIS 0.005 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5870) covalent geometry : angle 0.58550 / 0.31 ( 7963) SS BOND : bond 0.00202 / 0.14 ( 14) SS BOND : angle 1.07444 / 0.74 ( 28) hydrogen bonds : bond 0.04040 / 2.83 ( 188) hydrogen bonds : angle 7.17640 / 4.92 ( 501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.224 Fit side-chains REVERT: C 629 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6416 (pt) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.3906 time to fit residues: 35.7983 Evaluate side-chains 88 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 631 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 56 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.185333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.163960 restraints weight = 6599.570| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.66 r_work: 0.3786 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5884 Z= 0.115 Angle : 0.550 5.312 7991 Z= 0.291 Chirality : 0.043 0.148 859 Planarity : 0.004 0.039 1035 Dihedral : 4.444 18.009 810 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.75 % Allowed : 15.26 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.33 (0.30), residues: 730 helix: -0.92 (1.27), residues: 15 sheet: 0.37 (0.35), residues: 236 loop : -0.48 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.011 0.001 TYR C 511 PHE 0.008 0.001 PHE C 165 TRP 0.008 0.001 TRP B 110 HIS 0.003 0.001 HIS C 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 5870) covalent geometry : angle 0.54836 / 0.29 ( 7963) SS BOND : bond 0.00152 / 0.11 ( 14) SS BOND : angle 0.90019 / 0.63 ( 28) hydrogen bonds : bond 0.03483 / 2.46 ( 188) hydrogen bonds : angle 6.72517 / 4.61 ( 501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.221 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.4075 time to fit residues: 37.7035 Evaluate side-chains 83 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 631 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 5 optimal weight: 0.0870 chunk 53 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.186930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164690 restraints weight = 6619.693| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.81 r_work: 0.3791 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5884 Z= 0.100 Angle : 0.534 5.011 7991 Z= 0.284 Chirality : 0.043 0.146 859 Planarity : 0.004 0.039 1035 Dihedral : 4.269 17.540 810 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.91 % Allowed : 16.69 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.17 (0.31), residues: 730 helix: -0.93 (1.25), residues: 15 sheet: 0.50 (0.34), residues: 245 loop : -0.40 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.010 0.001 TYR C 511 PHE 0.008 0.001 PHE C 165 TRP 0.007 0.001 TRP B 110 HIS 0.003 0.001 HIS C 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 5870) covalent geometry : angle 0.53316 / 0.28 ( 7963) SS BOND : bond 0.00155 / 0.11 ( 14) SS BOND : angle 0.81316 / 0.58 ( 28) hydrogen bonds : bond 0.03180 / 2.25 ( 188) hydrogen bonds : angle 6.36848 / 4.36 ( 501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.160 Fit side-chains REVERT: C 281 VAL cc_start: 0.7991 (t) cc_final: 0.7711 (p) outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 0.4260 time to fit residues: 37.5582 Evaluate side-chains 77 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 480 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 127 HIS C 661 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.183395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160537 restraints weight = 6699.357| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.83 r_work: 0.3735 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5884 Z= 0.159 Angle : 0.599 7.801 7991 Z= 0.313 Chirality : 0.044 0.148 859 Planarity : 0.004 0.040 1035 Dihedral : 4.471 16.578 810 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.02 % Allowed : 16.53 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.27 (0.30), residues: 730 helix: -1.20 (1.21), residues: 15 sheet: 0.41 (0.34), residues: 245 loop : -0.45 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 78 TYR 0.009 0.001 TYR C 511 PHE 0.011 0.001 PHE C 165 TRP 0.008 0.001 TRP B 110 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 5870) covalent geometry : angle 0.59690 / 0.31 ( 7963) SS BOND : bond 0.00225 / 0.16 ( 14) SS BOND : angle 0.96884 / 0.65 ( 28) hydrogen bonds : bond 0.03437 / 2.41 ( 188) hydrogen bonds : angle 6.51011 / 4.46 ( 501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.224 Fit side-chains REVERT: C 246 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7179 (ptt) REVERT: C 629 ILE cc_start: 0.6547 (OUTLIER) cc_final: 0.6303 (pt) outliers start: 19 outliers final: 13 residues processed: 89 average time/residue: 0.3995 time to fit residues: 37.8309 Evaluate side-chains 89 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.0040 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.186409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164078 restraints weight = 6659.257| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.78 r_work: 0.3772 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5884 Z= 0.103 Angle : 0.545 7.200 7991 Z= 0.286 Chirality : 0.042 0.142 859 Planarity : 0.004 0.039 1035 Dihedral : 4.291 15.935 810 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.70 % Allowed : 17.81 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.19 (0.31), residues: 730 helix: -0.95 (1.12), residues: 21 sheet: 0.49 (0.34), residues: 246 loop : -0.41 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.015 0.001 TYR D 59 PHE 0.009 0.001 PHE C 165 TRP 0.008 0.001 TRP D 36 HIS 0.003 0.001 HIS C 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 5870) covalent geometry : angle 0.54367 / 0.29 ( 7963) SS BOND : bond 0.00168 / 0.11 ( 14) SS BOND : angle 0.78823 / 0.54 ( 28) hydrogen bonds : bond 0.03027 / 2.14 ( 188) hydrogen bonds : angle 6.13382 / 4.20 ( 501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.190 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 89 average time/residue: 0.3971 time to fit residues: 37.5918 Evaluate side-chains 85 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 70 ASN D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.183192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160273 restraints weight = 6615.065| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.88 r_work: 0.3730 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5884 Z= 0.167 Angle : 0.602 7.647 7991 Z= 0.315 Chirality : 0.044 0.146 859 Planarity : 0.004 0.040 1035 Dihedral : 4.489 16.907 810 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.18 % Allowed : 17.17 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.32 (0.30), residues: 730 helix: -1.13 (1.24), residues: 15 sheet: 0.40 (0.33), residues: 255 loop : -0.51 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 87 TYR 0.020 0.002 TYR D 59 PHE 0.010 0.001 PHE C 165 TRP 0.008 0.001 TRP B 110 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 5870) covalent geometry : angle 0.59976 / 0.31 ( 7963) SS BOND : bond 0.00240 / 0.17 ( 14) SS BOND : angle 0.99485 / 0.66 ( 28) hydrogen bonds : bond 0.03450 / 2.43 ( 188) hydrogen bonds : angle 6.38842 / 4.37 ( 501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.173 Fit side-chains REVERT: A 103 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6890 (mmtp) REVERT: C 231 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8069 (mt-10) outliers start: 20 outliers final: 15 residues processed: 87 average time/residue: 0.4048 time to fit residues: 37.2647 Evaluate side-chains 92 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 661 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.183894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162111 restraints weight = 6689.925| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.72 r_work: 0.3756 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5884 Z= 0.140 Angle : 0.583 7.275 7991 Z= 0.305 Chirality : 0.043 0.143 859 Planarity : 0.004 0.040 1035 Dihedral : 4.455 16.629 810 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.70 % Allowed : 18.12 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.32 (0.31), residues: 730 helix: -1.13 (1.23), residues: 15 sheet: 0.33 (0.34), residues: 236 loop : -0.44 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.020 0.001 TYR D 59 PHE 0.011 0.001 PHE C 165 TRP 0.008 0.001 TRP B 110 HIS 0.003 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 5870) covalent geometry : angle 0.57882 / 0.30 ( 7963) SS BOND : bond 0.00210 / 0.14 ( 14) SS BOND : angle 1.31792 / 0.79 ( 28) hydrogen bonds : bond 0.03262 / 2.30 ( 188) hydrogen bonds : angle 6.30580 / 4.32 ( 501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.162 Fit side-chains REVERT: A 103 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6897 (mmtp) REVERT: C 231 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8061 (mt-10) outliers start: 17 outliers final: 16 residues processed: 85 average time/residue: 0.4101 time to fit residues: 37.0773 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 661 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.181527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158924 restraints weight = 6727.078| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.82 r_work: 0.3732 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5884 Z= 0.164 Angle : 0.601 7.346 7991 Z= 0.315 Chirality : 0.044 0.145 859 Planarity : 0.004 0.039 1035 Dihedral : 4.524 17.124 810 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.18 % Allowed : 17.97 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.32 (0.31), residues: 730 helix: -1.17 (1.23), residues: 15 sheet: 0.33 (0.34), residues: 246 loop : -0.45 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.020 0.001 TYR D 59 PHE 0.011 0.001 PHE C 165 TRP 0.008 0.001 TRP B 110 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 5870) covalent geometry : angle 0.59812 / 0.31 ( 7963) SS BOND : bond 0.00238 / 0.16 ( 14) SS BOND : angle 1.19699 / 0.77 ( 28) hydrogen bonds : bond 0.03370 / 2.37 ( 188) hydrogen bonds : angle 6.37311 / 4.37 ( 501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.240 Fit side-chains REVERT: A 103 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6727 (mmtp) REVERT: C 231 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: C 629 ILE cc_start: 0.6547 (OUTLIER) cc_final: 0.6326 (pt) outliers start: 20 outliers final: 17 residues processed: 88 average time/residue: 0.3806 time to fit residues: 35.8459 Evaluate side-chains 93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 0.0030 chunk 25 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 661 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.183305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.160901 restraints weight = 6580.053| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.82 r_work: 0.3757 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5884 Z= 0.121 Angle : 0.568 7.026 7991 Z= 0.297 Chirality : 0.043 0.141 859 Planarity : 0.004 0.040 1035 Dihedral : 4.403 16.473 810 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.38 % Allowed : 18.76 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.20 (0.31), residues: 730 helix: -1.06 (1.24), residues: 15 sheet: 0.35 (0.33), residues: 254 loop : -0.34 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 24 TYR 0.020 0.001 TYR D 59 PHE 0.010 0.001 PHE C 165 TRP 0.007 0.001 TRP B 110 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 5870) covalent geometry : angle 0.56602 / 0.30 ( 7963) SS BOND : bond 0.00158 / 0.11 ( 14) SS BOND : angle 1.00810 / 0.66 ( 28) hydrogen bonds : bond 0.03135 / 2.22 ( 188) hydrogen bonds : angle 6.19832 / 4.24 ( 501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1935.42 seconds wall clock time: 33 minutes 55.80 seconds (2035.80 seconds total)