Starting phenix.real_space_refine on Wed Jun 3 20:05:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rih_53995/06_2026/9rih_53995.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rih_53995/06_2026/9rih_53995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rih_53995/06_2026/9rih_53995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rih_53995/06_2026/9rih_53995.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rih_53995/06_2026/9rih_53995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rih_53995/06_2026/9rih_53995.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 42 5.16 5 C 5278 2.51 5 N 1395 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8315 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2246 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 266} Chain breaks: 1 Chain: "B" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1898 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 226} Chain: "C" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1867 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 223} Chain: "D" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.27 Number of scatterers: 8315 At special positions: 0 Unit cell: (97.2, 110.7, 106.65, 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 42 16.00 O 1600 8.00 N 1395 7.00 C 5278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.00 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 110 " 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: 0.79 Conformation dependent library (CDL) restraints added in 469.9 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 17 sheets defined 12.9% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 75 through 78 removed outlier: 3.581A pdb=" N THR A 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.555A pdb=" N TRP A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 4.720A pdb=" N LEU A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 221 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 4.087A pdb=" N ILE A 284 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.514A pdb=" N GLN B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 171 through 178 removed outlier: 4.557A pdb=" N THR B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 removed outlier: 4.297A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 70 removed outlier: 3.612A pdb=" N LEU C 69 " --> pdb=" O MET C 66 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.814A pdb=" N LEU C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.191A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 removed outlier: 4.467A pdb=" N ALA C 216 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 95 removed outlier: 5.957A pdb=" N LEU A 89 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET A 253 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 258 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 130 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 260 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR A 128 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 262 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE A 126 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 22 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 removed outlier: 4.772A pdb=" N PHE A 126 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 262 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR A 128 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 260 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG A 130 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 258 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 260 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 106 through 110 Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.419A pdb=" N ILE B 32 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS B 99 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY B 247 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 101 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 245 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 103 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B 243 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 232 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU B 70 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE B 234 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR B 68 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 236 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.609A pdb=" N VAL B 217 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA B 121 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN B 119 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 82 through 87 removed outlier: 6.615A pdb=" N LEU C 82 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR C 198 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS C 130 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN C 201 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR C 128 " --> pdb=" O ASN C 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 178 through 179 removed outlier: 7.090A pdb=" N LEU C 228 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 111 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET C 226 " --> pdb=" O TRP C 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.514A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.514A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.710A pdb=" N VAL H 94 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TRP H 36 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.909A pdb=" N ARG H 99 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP H 122 " --> pdb=" O ARG H 99 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2680 1.34 - 1.46: 2035 1.46 - 1.58: 3759 1.58 - 1.70: 0 1.70 - 1.81: 63 Bond restraints: 8537 Sorted by residual: bond pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " ideal model delta sigma weight residual 1.334 1.469 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C ASN A 102 " pdb=" O ASN A 102 " ideal model delta sigma weight residual 1.235 1.247 -0.012 4.70e-03 4.53e+04 6.43e+00 bond pdb=" C3 SPH A 301 " pdb=" O3 SPH A 301 " ideal model delta sigma weight residual 1.438 1.410 0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" CA ARG B 249 " pdb=" CB ARG B 249 " ideal model delta sigma weight residual 1.539 1.521 0.018 1.36e-02 5.41e+03 1.68e+00 bond pdb=" C ARG B 249 " pdb=" O ARG B 249 " ideal model delta sigma weight residual 1.235 1.225 0.010 9.00e-03 1.23e+04 1.30e+00 ... (remaining 8532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 11585 2.73 - 5.46: 67 5.46 - 8.19: 3 8.19 - 10.92: 2 10.92 - 13.65: 1 Bond angle restraints: 11658 Sorted by residual: angle pdb=" N ASP H 112 " pdb=" CA ASP H 112 " pdb=" C ASP H 112 " ideal model delta sigma weight residual 108.96 95.31 13.65 1.59e+00 3.96e-01 7.37e+01 angle pdb=" C ASP H 112 " pdb=" CA ASP H 112 " pdb=" CB ASP H 112 " ideal model delta sigma weight residual 110.22 119.45 -9.23 1.67e+00 3.59e-01 3.05e+01 angle pdb=" N ASP L 94 " pdb=" CA ASP L 94 " pdb=" C ASP L 94 " ideal model delta sigma weight residual 112.45 107.03 5.42 1.39e+00 5.18e-01 1.52e+01 angle pdb=" N GLY H 113 " pdb=" CA GLY H 113 " pdb=" C GLY H 113 " ideal model delta sigma weight residual 112.34 104.68 7.66 2.04e+00 2.40e-01 1.41e+01 angle pdb=" C ASP L 93 " pdb=" CA ASP L 93 " pdb=" CB ASP L 93 " ideal model delta sigma weight residual 109.80 115.58 -5.78 1.64e+00 3.72e-01 1.24e+01 ... (remaining 11653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 4777 16.96 - 33.91: 218 33.91 - 50.87: 48 50.87 - 67.82: 10 67.82 - 84.78: 2 Dihedral angle restraints: 5055 sinusoidal: 1948 harmonic: 3107 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 53.19 39.81 1 1.00e+01 1.00e-02 2.23e+01 dihedral pdb=" CA TYR H 34 " pdb=" C TYR H 34 " pdb=" N TYR H 35 " pdb=" CA TYR H 35 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE A 131 " pdb=" C PHE A 131 " pdb=" N ASP A 132 " pdb=" CA ASP A 132 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 802 0.032 - 0.064: 326 0.064 - 0.096: 98 0.096 - 0.127: 66 0.127 - 0.159: 8 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ILE B 234 " pdb=" N ILE B 234 " pdb=" C ILE B 234 " pdb=" CB ILE B 234 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ASN A 228 " pdb=" N ASN A 228 " pdb=" C ASN A 228 " pdb=" CB ASN A 228 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE C 169 " pdb=" N ILE C 169 " pdb=" C ILE C 169 " pdb=" CB ILE C 169 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1297 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH A 301 " 0.071 2.00e-02 2.50e+03 7.03e-02 4.95e+01 pdb=" C4 SPH A 301 " -0.073 2.00e-02 2.50e+03 pdb=" C5 SPH A 301 " -0.068 2.00e-02 2.50e+03 pdb=" C6 SPH A 301 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 232 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO B 233 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 200 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C THR C 200 " -0.022 2.00e-02 2.50e+03 pdb=" O THR C 200 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN C 201 " 0.008 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1339 2.77 - 3.30: 7496 3.30 - 3.83: 13985 3.83 - 4.37: 17356 4.37 - 4.90: 29549 Nonbonded interactions: 69725 Sorted by model distance: nonbonded pdb=" OE2 GLU A 134 " pdb=" OG SER C 21 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR B 130 " pdb=" O LEU B 166 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU A 51 " pdb=" OG SER C 163 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR B 176 " pdb=" O GLU C 50 " model vdw 2.242 3.040 nonbonded pdb=" O ARG H 32 " pdb=" OH TYR H 54 " model vdw 2.251 3.040 ... (remaining 69720 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: 4.300 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: 9.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.003 0.135 8540 Z= 0.143 Angle : 0.553 13.650 11664 Z= 0.296 Chirality : 0.043 0.159 1300 Planarity : 0.005 0.070 1508 Dihedral : 10.550 84.778 3058 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.21 % Allowed : 5.81 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.24), residues: 1062 helix: -2.77 (0.51), residues: 77 sheet: -0.41 (0.28), residues: 304 loop : -0.98 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 178 TYR 0.013 0.001 TYR C 188 PHE 0.010 0.001 PHE B 212 TRP 0.008 0.001 TRP A 109 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 8537) covalent geometry : angle 0.55050 / 0.30 (11658) SS BOND : bond 0.01510 / 0.72 ( 3) SS BOND : angle 2.49310 / 1.15 ( 6) hydrogen bonds : bond 0.15574 / 10.27 ( 241) hydrogen bonds : angle 7.22737 / 5.09 ( 642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.334 Fit side-chains REVERT: A 22 GLN cc_start: 0.6850 (mt0) cc_final: 0.6523 (tt0) REVERT: A 43 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7296 (mt-10) REVERT: A 60 ASP cc_start: 0.8183 (m-30) cc_final: 0.7922 (m-30) REVERT: A 145 GLN cc_start: 0.8817 (mt0) cc_final: 0.8436 (mt0) REVERT: A 202 GLN cc_start: 0.9314 (pt0) cc_final: 0.9085 (pt0) REVERT: A 282 ASP cc_start: 0.7658 (m-30) cc_final: 0.7450 (m-30) REVERT: B 76 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8285 (mtmt) REVERT: B 241 MET cc_start: 0.9164 (mtp) cc_final: 0.8929 (mtm) REVERT: B 249 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8606 (ptt90) REVERT: C 7 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8881 (mmtp) REVERT: C 43 LEU cc_start: 0.9316 (mt) cc_final: 0.9114 (mt) REVERT: C 67 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8627 (mt-10) REVERT: C 126 MET cc_start: 0.9280 (mmm) cc_final: 0.9075 (mmt) REVERT: C 217 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9070 (mp) REVERT: C 242 GLN cc_start: 0.6655 (pm20) cc_final: 0.6356 (mm-40) REVERT: D 47 LYS cc_start: 0.9100 (mttm) cc_final: 0.8889 (mttm) REVERT: H 32 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7395 (mtt180) REVERT: H 118 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.7966 (p0) outliers start: 11 outliers final: 4 residues processed: 176 average time/residue: 0.1120 time to fit residues: 26.0272 Evaluate side-chains 138 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN C 11 ASN C 97 GLN C 103 GLN C 221 GLN C 234 HIS L 6 GLN H 104 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.138531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.091123 restraints weight = 10022.724| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.56 r_work: 0.2705 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 8540 Z= 0.309 Angle : 0.626 5.935 11664 Z= 0.327 Chirality : 0.049 0.205 1300 Planarity : 0.006 0.056 1508 Dihedral : 6.472 58.560 1198 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.07 % Allowed : 9.10 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.24), residues: 1062 helix: -2.79 (0.47), residues: 82 sheet: -0.43 (0.27), residues: 316 loop : -1.05 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 182 TYR 0.014 0.002 TYR C 188 PHE 0.012 0.002 PHE B 203 TRP 0.009 0.002 TRP B 182 HIS 0.006 0.002 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.31 ( 8537) covalent geometry : angle 0.62634 / 0.33 (11658) SS BOND : bond 0.00160 / 0.07 ( 3) SS BOND : angle 0.46559 / 0.26 ( 6) hydrogen bonds : bond 0.04200 / 2.83 ( 241) hydrogen bonds : angle 6.48838 / 4.59 ( 642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.328 Fit side-chains REVERT: A 22 GLN cc_start: 0.6953 (mt0) cc_final: 0.6708 (tt0) REVERT: A 43 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 60 ASP cc_start: 0.8435 (m-30) cc_final: 0.8205 (m-30) REVERT: A 282 ASP cc_start: 0.8063 (m-30) cc_final: 0.7787 (m-30) REVERT: B 76 LYS cc_start: 0.8944 (mmtp) cc_final: 0.8706 (mttp) REVERT: B 226 GLN cc_start: 0.8442 (tp40) cc_final: 0.8216 (tm-30) REVERT: B 250 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8630 (pt0) REVERT: C 57 ASN cc_start: 0.9219 (p0) cc_final: 0.8923 (p0) REVERT: C 126 MET cc_start: 0.9430 (mmm) cc_final: 0.9182 (mmt) REVERT: C 182 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8092 (mtm180) REVERT: C 217 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9088 (mp) REVERT: C 242 GLN cc_start: 0.6735 (pm20) cc_final: 0.6488 (mm-40) REVERT: H 118 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.6726 (p0) outliers start: 28 outliers final: 20 residues processed: 145 average time/residue: 0.1041 time to fit residues: 20.1536 Evaluate side-chains 148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.143055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.098769 restraints weight = 9809.044| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.07 r_work: 0.2766 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8540 Z= 0.094 Angle : 0.481 5.694 11664 Z= 0.252 Chirality : 0.042 0.141 1300 Planarity : 0.004 0.041 1508 Dihedral : 5.886 59.977 1193 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.96 % Allowed : 9.98 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.24), residues: 1062 helix: -2.35 (0.50), residues: 83 sheet: -0.20 (0.28), residues: 295 loop : -0.95 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 182 TYR 0.011 0.001 TYR A 116 PHE 0.010 0.001 PHE B 212 TRP 0.011 0.001 TRP C 197 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 8537) covalent geometry : angle 0.48118 / 0.25 (11658) SS BOND : bond 0.00092 / 0.04 ( 3) SS BOND : angle 0.51531 / 0.29 ( 6) hydrogen bonds : bond 0.03235 / 2.18 ( 241) hydrogen bonds : angle 5.92344 / 4.24 ( 642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7060 (mt0) cc_final: 0.6834 (tt0) REVERT: A 43 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7922 (mt-10) REVERT: A 60 ASP cc_start: 0.8406 (m-30) cc_final: 0.8172 (m-30) REVERT: A 202 GLN cc_start: 0.9224 (pt0) cc_final: 0.9024 (pt0) REVERT: A 282 ASP cc_start: 0.8039 (m-30) cc_final: 0.7774 (m-30) REVERT: B 76 LYS cc_start: 0.8919 (mmtp) cc_final: 0.8414 (mtmt) REVERT: C 177 TYR cc_start: 0.9319 (m-80) cc_final: 0.9087 (m-80) REVERT: C 182 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8084 (mtm110) REVERT: C 217 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9107 (mp) REVERT: D 47 LYS cc_start: 0.8942 (mttp) cc_final: 0.8598 (mttm) REVERT: H 118 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.6495 (p0) outliers start: 27 outliers final: 20 residues processed: 149 average time/residue: 0.0985 time to fit residues: 19.8247 Evaluate side-chains 148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 226 GLN C 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.139856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.092637 restraints weight = 10179.797| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.58 r_work: 0.2729 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8540 Z= 0.236 Angle : 0.561 5.834 11664 Z= 0.291 Chirality : 0.046 0.174 1300 Planarity : 0.005 0.044 1508 Dihedral : 6.117 55.617 1193 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.28 % Allowed : 8.66 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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 (0.24), residues: 1062 helix: -2.47 (0.50), residues: 82 sheet: -0.29 (0.28), residues: 309 loop : -0.96 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 186 TYR 0.019 0.002 TYR D 37 PHE 0.012 0.002 PHE B 203 TRP 0.007 0.001 TRP C 157 HIS 0.004 0.001 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 ( 8537) covalent geometry : angle 0.56077 / 0.29 (11658) SS BOND : bond 0.00110 / 0.04 ( 3) SS BOND : angle 0.45525 / 0.24 ( 6) hydrogen bonds : bond 0.03652 / 2.47 ( 241) hydrogen bonds : angle 6.14651 / 4.38 ( 642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.295 Fit side-chains REVERT: A 22 GLN cc_start: 0.6971 (mt0) cc_final: 0.6710 (tt0) REVERT: A 43 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7776 (mt-10) REVERT: A 60 ASP cc_start: 0.8508 (m-30) cc_final: 0.8265 (m-30) REVERT: A 218 LYS cc_start: 0.8139 (mttp) cc_final: 0.7788 (mmmm) REVERT: A 282 ASP cc_start: 0.8078 (m-30) cc_final: 0.7799 (m-30) REVERT: B 76 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8693 (mttp) REVERT: B 250 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8588 (pt0) REVERT: C 57 ASN cc_start: 0.9194 (p0) cc_final: 0.8895 (p0) REVERT: C 177 TYR cc_start: 0.9370 (m-80) cc_final: 0.9154 (m-80) REVERT: C 217 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9147 (mp) REVERT: C 242 GLN cc_start: 0.6678 (pm20) cc_final: 0.6448 (mm-40) REVERT: H 118 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.6643 (p0) outliers start: 39 outliers final: 29 residues processed: 153 average time/residue: 0.1074 time to fit residues: 22.0091 Evaluate side-chains 154 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 226 GLN C 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.141939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.097850 restraints weight = 10043.975| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.91 r_work: 0.2775 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8540 Z= 0.116 Angle : 0.492 6.766 11664 Z= 0.256 Chirality : 0.043 0.144 1300 Planarity : 0.004 0.040 1508 Dihedral : 5.884 54.821 1193 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.07 % Allowed : 10.42 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.24), residues: 1062 helix: -2.34 (0.50), residues: 82 sheet: -0.16 (0.28), residues: 296 loop : -0.91 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 182 TYR 0.012 0.001 TYR D 37 PHE 0.009 0.001 PHE B 212 TRP 0.008 0.001 TRP C 197 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8537) covalent geometry : angle 0.49226 / 0.26 (11658) SS BOND : bond 0.00075 / 0.03 ( 3) SS BOND : angle 0.47711 / 0.26 ( 6) hydrogen bonds : bond 0.03186 / 2.16 ( 241) hydrogen bonds : angle 5.90538 / 4.23 ( 642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7037 (mt0) cc_final: 0.6817 (tt0) REVERT: A 43 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7729 (mt-10) REVERT: A 60 ASP cc_start: 0.8415 (m-30) cc_final: 0.8202 (m-30) REVERT: A 282 ASP cc_start: 0.8048 (m-30) cc_final: 0.7756 (m-30) REVERT: C 182 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.7839 (mtm180) REVERT: C 217 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9083 (mp) REVERT: H 118 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.6613 (p0) outliers start: 28 outliers final: 21 residues processed: 141 average time/residue: 0.1115 time to fit residues: 21.0662 Evaluate side-chains 155 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 50.0000 chunk 73 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 17 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 226 GLN C 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.141169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.097169 restraints weight = 9945.335| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.94 r_work: 0.2761 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8540 Z= 0.162 Angle : 0.509 5.814 11664 Z= 0.264 Chirality : 0.044 0.153 1300 Planarity : 0.005 0.038 1508 Dihedral : 5.890 50.616 1193 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.51 % Allowed : 10.96 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.20 (0.25), residues: 1062 helix: -2.31 (0.51), residues: 82 sheet: -0.27 (0.28), residues: 316 loop : -0.84 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 182 TYR 0.015 0.001 TYR D 37 PHE 0.010 0.001 PHE B 212 TRP 0.006 0.001 TRP C 157 HIS 0.003 0.001 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 8537) covalent geometry : angle 0.50881 / 0.26 (11658) SS BOND : bond 0.00078 / 0.03 ( 3) SS BOND : angle 0.41200 / 0.22 ( 6) hydrogen bonds : bond 0.03311 / 2.24 ( 241) hydrogen bonds : angle 5.90567 / 4.23 ( 642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.6920 (mt0) cc_final: 0.6657 (tt0) REVERT: A 43 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7725 (mt-10) REVERT: A 60 ASP cc_start: 0.8459 (m-30) cc_final: 0.8258 (m-30) REVERT: A 282 ASP cc_start: 0.8046 (m-30) cc_final: 0.7755 (m-30) REVERT: B 250 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: C 182 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.7840 (mtm180) REVERT: C 217 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9104 (mp) REVERT: C 242 GLN cc_start: 0.6724 (pm20) cc_final: 0.6399 (mm-40) REVERT: H 118 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.6585 (p0) outliers start: 32 outliers final: 26 residues processed: 154 average time/residue: 0.1084 time to fit residues: 22.3029 Evaluate side-chains 155 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 0.0020 chunk 85 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 40.0000 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.141503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.097111 restraints weight = 10061.468| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.93 r_work: 0.2764 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8540 Z= 0.154 Angle : 0.512 8.361 11664 Z= 0.264 Chirality : 0.044 0.150 1300 Planarity : 0.004 0.039 1508 Dihedral : 5.877 49.093 1193 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.06 % Allowed : 11.18 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.16 (0.25), residues: 1062 helix: -2.27 (0.51), residues: 82 sheet: -0.21 (0.28), residues: 315 loop : -0.83 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.017 0.001 TYR D 37 PHE 0.009 0.001 PHE B 212 TRP 0.006 0.001 TRP A 109 HIS 0.002 0.001 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 8537) covalent geometry : angle 0.51206 / 0.26 (11658) SS BOND : bond 0.00072 / 0.03 ( 3) SS BOND : angle 0.46288 / 0.26 ( 6) hydrogen bonds : bond 0.03266 / 2.21 ( 241) hydrogen bonds : angle 5.85685 / 4.19 ( 642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.322 Fit side-chains REVERT: A 22 GLN cc_start: 0.6898 (mt0) cc_final: 0.6642 (tt0) REVERT: A 43 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 60 ASP cc_start: 0.8460 (m-30) cc_final: 0.8256 (m-30) REVERT: A 218 LYS cc_start: 0.8349 (mttp) cc_final: 0.8043 (mmmm) REVERT: A 282 ASP cc_start: 0.8053 (m-30) cc_final: 0.7754 (m-30) REVERT: B 250 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: C 182 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.7912 (mtm180) REVERT: C 217 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9091 (mp) REVERT: C 231 ASP cc_start: 0.8312 (m-30) cc_final: 0.8014 (m-30) REVERT: H 118 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.6614 (p0) outliers start: 37 outliers final: 30 residues processed: 152 average time/residue: 0.1056 time to fit residues: 21.6609 Evaluate side-chains 165 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 8.9990 chunk 66 optimal weight: 0.0670 chunk 88 optimal weight: 40.0000 chunk 101 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 83 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 overall best weight: 3.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.141175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.096338 restraints weight = 10004.399| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.07 r_work: 0.2741 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8540 Z= 0.171 Angle : 0.520 7.417 11664 Z= 0.269 Chirality : 0.044 0.157 1300 Planarity : 0.005 0.040 1508 Dihedral : 5.936 49.753 1193 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.28 % Allowed : 11.07 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.16 (0.25), residues: 1062 helix: -2.25 (0.51), residues: 82 sheet: -0.21 (0.28), residues: 316 loop : -0.83 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.017 0.001 TYR D 37 PHE 0.009 0.001 PHE B 212 TRP 0.006 0.001 TRP C 157 HIS 0.003 0.001 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 8537) covalent geometry : angle 0.52003 / 0.27 (11658) SS BOND : bond 0.00082 / 0.03 ( 3) SS BOND : angle 0.42346 / 0.23 ( 6) hydrogen bonds : bond 0.03317 / 2.24 ( 241) hydrogen bonds : angle 5.87018 / 4.20 ( 642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.345 Fit side-chains REVERT: A 22 GLN cc_start: 0.6947 (mt0) cc_final: 0.6696 (tt0) REVERT: A 43 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 60 ASP cc_start: 0.8521 (m-30) cc_final: 0.8320 (m-30) REVERT: A 218 LYS cc_start: 0.8386 (mttp) cc_final: 0.8076 (mmmm) REVERT: A 282 ASP cc_start: 0.8086 (m-30) cc_final: 0.7798 (m-30) REVERT: B 250 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: C 217 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9101 (mp) REVERT: C 231 ASP cc_start: 0.8357 (m-30) cc_final: 0.8072 (m-30) REVERT: C 242 GLN cc_start: 0.6800 (pm20) cc_final: 0.6468 (mm-40) REVERT: H 118 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.6647 (p0) outliers start: 39 outliers final: 35 residues processed: 156 average time/residue: 0.1031 time to fit residues: 21.7071 Evaluate side-chains 161 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 9.9990 chunk 52 optimal weight: 0.0050 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.140341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.095909 restraints weight = 10031.579| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.95 r_work: 0.2737 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8540 Z= 0.235 Angle : 0.562 6.803 11664 Z= 0.290 Chirality : 0.046 0.176 1300 Planarity : 0.005 0.044 1508 Dihedral : 6.207 51.626 1193 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.17 % Allowed : 11.40 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.20 (0.25), residues: 1062 helix: -2.24 (0.52), residues: 82 sheet: -0.22 (0.29), residues: 316 loop : -0.88 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 182 TYR 0.019 0.002 TYR D 37 PHE 0.012 0.002 PHE B 203 TRP 0.008 0.001 TRP C 157 HIS 0.004 0.001 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 ( 8537) covalent geometry : angle 0.56206 / 0.29 (11658) SS BOND : bond 0.00118 / 0.04 ( 3) SS BOND : angle 0.48882 / 0.26 ( 6) hydrogen bonds : bond 0.03551 / 2.40 ( 241) hydrogen bonds : angle 6.00209 / 4.29 ( 642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.298 Fit side-chains REVERT: A 22 GLN cc_start: 0.6881 (mt0) cc_final: 0.6625 (tt0) REVERT: A 43 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 60 ASP cc_start: 0.8507 (m-30) cc_final: 0.8294 (m-30) REVERT: A 282 ASP cc_start: 0.8065 (m-30) cc_final: 0.7758 (m-30) REVERT: B 76 LYS cc_start: 0.8980 (mttp) cc_final: 0.8629 (mtmt) REVERT: B 250 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8594 (pt0) REVERT: C 182 ARG cc_start: 0.8629 (mtm-85) cc_final: 0.8013 (mtm180) REVERT: C 217 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9122 (mp) REVERT: C 231 ASP cc_start: 0.8325 (m-30) cc_final: 0.8025 (m-30) REVERT: C 242 GLN cc_start: 0.6707 (pm20) cc_final: 0.6423 (mm-40) REVERT: H 118 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.6627 (p0) outliers start: 38 outliers final: 35 residues processed: 145 average time/residue: 0.1004 time to fit residues: 19.6297 Evaluate side-chains 157 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 50.0000 chunk 98 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 91 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.142283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.098112 restraints weight = 9916.691| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.12 r_work: 0.2767 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8540 Z= 0.118 Angle : 0.497 7.090 11664 Z= 0.258 Chirality : 0.043 0.142 1300 Planarity : 0.004 0.038 1508 Dihedral : 5.937 49.580 1193 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.62 % Allowed : 12.28 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.14 (0.25), residues: 1062 helix: -2.17 (0.52), residues: 82 sheet: -0.17 (0.29), residues: 314 loop : -0.84 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.015 0.001 TYR D 37 PHE 0.009 0.001 PHE B 212 TRP 0.008 0.001 TRP C 197 HIS 0.002 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8537) covalent geometry : angle 0.49749 / 0.26 (11658) SS BOND : bond 0.00054 / 0.02 ( 3) SS BOND : angle 0.45204 / 0.25 ( 6) hydrogen bonds : bond 0.03136 / 2.12 ( 241) hydrogen bonds : angle 5.76815 / 4.14 ( 642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.273 Fit side-chains REVERT: A 43 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 218 LYS cc_start: 0.8162 (mttp) cc_final: 0.7780 (mmmt) REVERT: A 282 ASP cc_start: 0.7999 (m-30) cc_final: 0.7724 (m-30) REVERT: B 76 LYS cc_start: 0.8958 (mttp) cc_final: 0.8658 (mtmt) REVERT: C 182 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8033 (mtm180) REVERT: C 217 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9099 (mp) REVERT: C 231 ASP cc_start: 0.8316 (m-30) cc_final: 0.8025 (m-30) REVERT: H 118 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.6632 (p0) outliers start: 33 outliers final: 31 residues processed: 144 average time/residue: 0.0974 time to fit residues: 18.8407 Evaluate side-chains 162 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 0.0070 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.141152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.096726 restraints weight = 10021.012| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.96 r_work: 0.2754 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8540 Z= 0.186 Angle : 0.532 6.578 11664 Z= 0.275 Chirality : 0.045 0.157 1300 Planarity : 0.005 0.041 1508 Dihedral : 6.139 51.802 1193 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.17 % Allowed : 11.73 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -1.15 (0.25), residues: 1062 helix: -2.16 (0.52), residues: 82 sheet: -0.17 (0.29), residues: 316 loop : -0.86 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 182 TYR 0.017 0.001 TYR D 37 PHE 0.011 0.001 PHE B 203 TRP 0.007 0.001 TRP C 157 HIS 0.003 0.001 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 8537) covalent geometry : angle 0.53214 / 0.27 (11658) SS BOND : bond 0.00079 / 0.03 ( 3) SS BOND : angle 0.46328 / 0.26 ( 6) hydrogen bonds : bond 0.03358 / 2.27 ( 241) hydrogen bonds : angle 5.87272 / 4.21 ( 642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.12 seconds wall clock time: 43 minutes 30.18 seconds (2610.18 seconds total)