Starting phenix.real_space_refine on Thu Oct 22 22:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23bx_68851/10_2026/23bx_68851.cif Found real_map, /net/cci-nas-00/data/ceres_data/23bx_68851/10_2026/23bx_68851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23bx_68851/10_2026/23bx_68851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23bx_68851/10_2026/23bx_68851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23bx_68851/10_2026/23bx_68851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23bx_68851/10_2026/23bx_68851.map" } resolution = 2.62 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= 0.007 sd= 0.038 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 4079 2.51 5 N 1085 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2312 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 277} Chain: "B" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1874 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1908 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 297 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} 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: 1.64, per 1000 atoms: 0.26 Number of scatterers: 6412 At special positions: 0 Unit cell: (92.169, 109.858, 82.859, 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 1209 8.00 N 1085 7.00 C 4079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 431.5 milliseconds 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 12 sheets defined 14.8% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.684A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.521A pdb=" N TRP A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A 163 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 164 " --> pdb=" O HIS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 164' Processing helix chain 'A' and resid 211 through 215 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 56 through 60 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 167 through 173 removed outlier: 4.267A pdb=" N THR B 171 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 removed outlier: 4.237A pdb=" N VAL C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 49 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 76 removed outlier: 6.582A pdb=" N VAL A 238 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS A 71 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 236 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 73 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 234 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A 75 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE A 232 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 245 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A 114 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 247 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 112 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 249 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE A 110 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 22 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 193 removed outlier: 4.867A pdb=" N PHE A 110 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 249 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 112 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 247 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A 114 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 245 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA A 247 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.135A pdb=" N ALA A 168 " --> pdb=" O PHE A 146 " (cutoff:3.500A) 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 32 through 33 removed outlier: 6.803A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.803A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B 226 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.619A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.895A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.270A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 516 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: 0.88 Time building geometry restraints manager: 0.76 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: 2086 1.34 - 1.46: 1423 1.46 - 1.58: 3001 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 6574 Sorted by residual: bond pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " ideal model delta sigma weight residual 1.334 1.470 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" CA GLU A 108 " pdb=" C GLU A 108 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.41e-02 5.03e+03 3.95e+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 2.00e+00 bond pdb=" CB GLU C 237 " pdb=" CG GLU C 237 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 ... (remaining 6569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8798 1.69 - 3.37: 135 3.37 - 5.06: 14 5.06 - 6.74: 4 6.74 - 8.43: 4 Bond angle restraints: 8955 Sorted by residual: angle pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " pdb=" CD GLU A 19 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.70e+00 3.46e-01 1.06e+01 angle pdb=" C SER A 129 " pdb=" N ASN A 130 " pdb=" CA ASN A 130 " ideal model delta sigma weight residual 121.90 118.00 3.90 1.26e+00 6.30e-01 9.57e+00 angle pdb=" CA GLU B 74 " pdb=" CB GLU B 74 " pdb=" CG GLU B 74 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.45e+00 angle pdb=" CA GLU A 19 " pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 114.10 119.82 -5.72 2.00e+00 2.50e-01 8.17e+00 angle pdb=" CB GLU C 237 " pdb=" CG GLU C 237 " pdb=" CD GLU C 237 " ideal model delta sigma weight residual 112.60 117.43 -4.83 1.70e+00 3.46e-01 8.08e+00 ... (remaining 8950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 3474 17.34 - 34.68: 309 34.68 - 52.01: 95 52.01 - 69.35: 31 69.35 - 86.69: 10 Dihedral angle restraints: 3919 sinusoidal: 1540 harmonic: 2379 Sorted by residual: dihedral pdb=" CA LEU C 86 " pdb=" C LEU C 86 " pdb=" N ASP C 87 " pdb=" CA ASP C 87 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP D 34 " pdb=" CB ASP D 34 " pdb=" CG ASP D 34 " pdb=" OD1 ASP D 34 " ideal model delta sinusoidal sigma weight residual -30.00 -84.17 54.17 1 2.00e+01 2.50e-03 9.95e+00 dihedral pdb=" CG ARG B 181 " pdb=" CD ARG B 181 " pdb=" NE ARG B 181 " pdb=" CZ ARG B 181 " ideal model delta sinusoidal sigma weight residual 90.00 131.85 -41.85 2 1.50e+01 4.44e-03 9.50e+00 ... (remaining 3916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 735 0.040 - 0.081: 189 0.081 - 0.121: 80 0.121 - 0.161: 4 0.161 - 0.202: 1 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CG LEU C 86 " pdb=" CB LEU C 86 " pdb=" CD1 LEU C 86 " pdb=" CD2 LEU C 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ASN C 60 " pdb=" N ASN C 60 " pdb=" C ASN C 60 " pdb=" CB ASN C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ASN A 131 " pdb=" N ASN A 131 " pdb=" C ASN A 131 " pdb=" CB ASN A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1006 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH A 301 " -0.087 2.00e-02 2.50e+03 8.67e-02 7.52e+01 pdb=" C4 SPH A 301 " 0.087 2.00e-02 2.50e+03 pdb=" C5 SPH A 301 " 0.087 2.00e-02 2.50e+03 pdb=" C6 SPH A 301 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 237 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" CD GLU C 237 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU C 237 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 237 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 57 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C THR A 57 " 0.025 2.00e-02 2.50e+03 pdb=" O THR A 57 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 58 " -0.009 2.00e-02 2.50e+03 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 3199 2.98 - 3.46: 6080 3.46 - 3.94: 10970 3.94 - 4.42: 12941 4.42 - 4.90: 20736 Nonbonded interactions: 53926 Sorted by model distance: nonbonded pdb=" N GLU A 19 " pdb=" OE1 GLU A 19 " model vdw 2.506 3.120 nonbonded pdb=" N GLU C 237 " pdb=" OE1 GLU C 237 " model vdw 2.517 3.120 nonbonded pdb=" N GLU A 284 " pdb=" OE1 GLU A 284 " model vdw 2.532 3.120 nonbonded pdb=" N GLU B 74 " pdb=" OE1 GLU B 74 " model vdw 2.547 3.120 nonbonded pdb=" N ASP C 220 " pdb=" OD1 ASP C 220 " model vdw 2.579 3.120 ... (remaining 53921 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: 0.710 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.400 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 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 0.136 6574 Z= 0.176 Angle : 0.535 8.425 8955 Z= 0.274 Chirality : 0.042 0.202 1009 Planarity : 0.004 0.087 1157 Dihedral : 16.157 86.688 2381 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.13 % Allowed : 19.61 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.03 (0.29), residues: 811 helix: -2.22 (0.57), residues: 67 sheet: 0.63 (0.36), residues: 212 loop : 0.16 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.009 0.001 TYR B 31 PHE 0.006 0.001 PHE B 200 TRP 0.004 0.001 TRP C 155 HIS 0.001 0.000 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 6574) covalent geometry : angle 0.53521 / 0.27 ( 8955) hydrogen bonds : bond 0.18735 / 12.51 ( 171) hydrogen bonds : angle 9.18610 / 6.56 ( 516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8957 (pttt) cc_final: 0.8485 (ptmm) REVERT: A 78 ASN cc_start: 0.7923 (p0) cc_final: 0.7703 (p0) REVERT: B 12 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7796 (mmm160) REVERT: B 52 LYS cc_start: 0.9360 (tttm) cc_final: 0.6951 (mppt) REVERT: B 91 MET cc_start: 0.8205 (mmt) cc_final: 0.7863 (mmm) REVERT: B 116 LYS cc_start: 0.9168 (mttm) cc_final: 0.7372 (mtmt) REVERT: B 206 GLN cc_start: 0.9274 (mp-120) cc_final: 0.8925 (mp10) REVERT: B 220 ARG cc_start: 0.9227 (mtp180) cc_final: 0.8992 (mtm180) REVERT: C 50 GLU cc_start: 0.9104 (pt0) cc_final: 0.8331 (mt-10) REVERT: C 114 GLU cc_start: 0.8800 (pp20) cc_final: 0.8310 (pp20) REVERT: C 205 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8194 (mt-10) outliers start: 8 outliers final: 7 residues processed: 121 average time/residue: 0.5780 time to fit residues: 73.1869 Evaluate side-chains 123 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN B 15 GLN B 45 HIS B 55 GLN B 206 GLN C 65 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 197 GLN D 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.091016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.075947 restraints weight = 10733.131| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.26 r_work: 0.2789 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6574 Z= 0.131 Angle : 0.470 8.551 8955 Z= 0.244 Chirality : 0.043 0.198 1009 Planarity : 0.004 0.025 1157 Dihedral : 5.771 54.069 903 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.40 % Allowed : 15.80 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.15 (0.29), residues: 811 helix: -1.88 (0.58), residues: 67 sheet: 0.82 (0.36), residues: 206 loop : 0.16 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.011 0.001 TYR B 31 PHE 0.008 0.001 PHE C 215 TRP 0.005 0.001 TRP A 248 HIS 0.002 0.000 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6574) covalent geometry : angle 0.47040 / 0.24 ( 8955) hydrogen bonds : bond 0.03523 / 2.39 ( 171) hydrogen bonds : angle 6.12924 / 4.33 ( 516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8980 (pttt) cc_final: 0.8499 (ptmm) REVERT: A 78 ASN cc_start: 0.7923 (p0) cc_final: 0.7696 (p0) REVERT: A 127 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8885 (p) REVERT: A 169 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.9000 (m) REVERT: B 12 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7686 (mmm160) REVERT: B 52 LYS cc_start: 0.9348 (tttm) cc_final: 0.7006 (mppt) REVERT: B 61 ASP cc_start: 0.8884 (m-30) cc_final: 0.8620 (m-30) REVERT: B 116 LYS cc_start: 0.9105 (mttm) cc_final: 0.7260 (mtmt) REVERT: C 148 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8769 (ppp) REVERT: C 196 MET cc_start: 0.9123 (mmt) cc_final: 0.8896 (mmm) REVERT: C 205 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8189 (mt-10) REVERT: D 42 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7952 (mttp) outliers start: 17 outliers final: 5 residues processed: 130 average time/residue: 0.5498 time to fit residues: 74.9917 Evaluate side-chains 127 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 42 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [60, 56, 12, 21, 15, 67, 34, 33, 1, 49, 50] chunk 60 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.074650 restraints weight = 10764.114| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.27 r_work: 0.2795 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6574 Z= 0.176 Angle : 0.493 8.416 8955 Z= 0.255 Chirality : 0.043 0.202 1009 Planarity : 0.004 0.027 1157 Dihedral : 5.517 58.940 895 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.82 % Allowed : 16.50 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.18 (0.29), residues: 811 helix: -1.67 (0.60), residues: 66 sheet: 0.83 (0.36), residues: 206 loop : 0.15 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.011 0.001 TYR B 31 PHE 0.009 0.001 PHE C 215 TRP 0.005 0.001 TRP B 177 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 6574) covalent geometry : angle 0.49298 / 0.25 ( 8955) hydrogen bonds : bond 0.03483 / 2.36 ( 171) hydrogen bonds : angle 5.80778 / 4.10 ( 516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9026 (pttt) cc_final: 0.8560 (ptmm) REVERT: A 78 ASN cc_start: 0.7962 (p0) cc_final: 0.7758 (p0) REVERT: B 12 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7824 (mmm160) REVERT: B 52 LYS cc_start: 0.9408 (tttm) cc_final: 0.7087 (mppt) REVERT: B 116 LYS cc_start: 0.9163 (mttm) cc_final: 0.7374 (mtmt) REVERT: B 235 MET cc_start: 0.9215 (mtp) cc_final: 0.8865 (mtp) REVERT: C 41 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.7927 (mtm180) REVERT: C 205 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8238 (mt-10) outliers start: 20 outliers final: 8 residues processed: 131 average time/residue: 0.5481 time to fit residues: 75.3723 Evaluate side-chains 126 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [33, 43, 72, 2, 52, 4, 36, 75, 58, 53, 30] chunk 33 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.088132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.073053 restraints weight = 10822.660| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.26 r_work: 0.2725 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6574 Z= 0.246 Angle : 0.517 8.109 8955 Z= 0.267 Chirality : 0.044 0.212 1009 Planarity : 0.004 0.029 1157 Dihedral : 5.644 56.085 895 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.39 % Allowed : 16.36 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.10 (0.28), residues: 811 helix: -1.68 (0.59), residues: 66 sheet: 0.90 (0.36), residues: 197 loop : 0.05 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.015 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.003 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 ( 6574) covalent geometry : angle 0.51671 / 0.27 ( 8955) hydrogen bonds : bond 0.03581 / 2.42 ( 171) hydrogen bonds : angle 5.75253 / 4.05 ( 516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9021 (pttt) cc_final: 0.8526 (ptmm) REVERT: A 88 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8215 (mmtm) REVERT: A 112 TYR cc_start: 0.9617 (m-80) cc_final: 0.9406 (m-80) REVERT: A 127 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8922 (p) REVERT: A 156 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8372 (ptmm) REVERT: B 12 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7754 (mmm160) REVERT: B 52 LYS cc_start: 0.9378 (tttm) cc_final: 0.7028 (mppt) REVERT: B 116 LYS cc_start: 0.9106 (mttm) cc_final: 0.7380 (mtmt) REVERT: C 41 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.7909 (mtm180) REVERT: C 205 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8125 (mt-10) REVERT: D 42 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7886 (mttp) outliers start: 24 outliers final: 13 residues processed: 135 average time/residue: 0.5395 time to fit residues: 76.6131 Evaluate side-chains 132 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 50 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [22, 21, 18, 1, 28, 26, 70, 8, 10, 58, 60] chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.088963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.073991 restraints weight = 10898.043| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.26 r_work: 0.2754 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6574 Z= 0.177 Angle : 0.500 8.488 8955 Z= 0.259 Chirality : 0.043 0.206 1009 Planarity : 0.004 0.028 1157 Dihedral : 5.293 46.681 895 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.24 % Allowed : 17.07 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.10 (0.28), residues: 811 helix: -1.59 (0.60), residues: 66 sheet: 0.87 (0.36), residues: 197 loop : 0.05 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.014 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.002 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 6574) covalent geometry : angle 0.49969 / 0.26 ( 8955) hydrogen bonds : bond 0.03253 / 2.22 ( 171) hydrogen bonds : angle 5.56396 / 3.92 ( 516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9013 (pttt) cc_final: 0.8513 (ptmm) REVERT: A 88 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8329 (mmtm) REVERT: A 127 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8873 (p) REVERT: A 156 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8373 (ptmm) REVERT: B 12 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7749 (mmm160) REVERT: B 52 LYS cc_start: 0.9402 (tttm) cc_final: 0.7070 (mppt) REVERT: B 116 LYS cc_start: 0.9097 (mttm) cc_final: 0.7346 (mtmt) REVERT: C 41 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.7890 (mtm180) REVERT: C 205 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8177 (mt-10) REVERT: D 42 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7858 (mttp) outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 0.5468 time to fit residues: 75.8348 Evaluate side-chains 127 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 50 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [27, 16, 68, 55, 44, 38, 67, 59, 70, 41, 50] chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 0.1980 chunk 41 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.088491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.073452 restraints weight = 10941.993| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.25 r_work: 0.2748 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6574 Z= 0.199 Angle : 0.508 8.403 8955 Z= 0.261 Chirality : 0.044 0.208 1009 Planarity : 0.004 0.028 1157 Dihedral : 5.015 36.515 895 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.95 % Allowed : 16.50 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.07 (0.28), residues: 811 helix: -1.60 (0.60), residues: 66 sheet: 0.82 (0.36), residues: 196 loop : 0.04 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 104 TYR 0.015 0.001 TYR B 31 PHE 0.009 0.001 PHE C 215 TRP 0.008 0.001 TRP B 177 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 6574) covalent geometry : angle 0.50776 / 0.26 ( 8955) hydrogen bonds : bond 0.03321 / 2.28 ( 171) hydrogen bonds : angle 5.52923 / 3.90 ( 516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 88 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8277 (mmtm) REVERT: A 127 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 131 ASN cc_start: 0.6229 (OUTLIER) cc_final: 0.6021 (p0) REVERT: A 156 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8326 (ptmm) REVERT: B 12 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7665 (mmm160) REVERT: B 52 LYS cc_start: 0.9368 (tttm) cc_final: 0.7013 (mppt) REVERT: B 116 LYS cc_start: 0.9049 (mttm) cc_final: 0.7279 (mtmt) REVERT: C 41 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.7880 (mtm180) REVERT: C 205 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8168 (mt-10) REVERT: D 42 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7864 (mttp) outliers start: 28 outliers final: 14 residues processed: 132 average time/residue: 0.5321 time to fit residues: 73.8191 Evaluate side-chains 135 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 50 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [78, 11, 43, 4, 27, 36, 33, 76, 6, 0, 14] chunk 78 optimal weight: 0.0770 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.088903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.073871 restraints weight = 10838.647| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.25 r_work: 0.2757 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6574 Z= 0.175 Angle : 0.525 8.474 8955 Z= 0.270 Chirality : 0.044 0.244 1009 Planarity : 0.004 0.028 1157 Dihedral : 4.878 30.449 895 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.10 % Allowed : 17.63 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.11 (0.28), residues: 811 helix: -1.56 (0.60), residues: 66 sheet: 0.81 (0.36), residues: 196 loop : 0.07 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.015 0.001 TYR B 31 PHE 0.009 0.001 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.002 0.001 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 6574) covalent geometry : angle 0.52529 / 0.27 ( 8955) hydrogen bonds : bond 0.03195 / 2.19 ( 171) hydrogen bonds : angle 5.46980 / 3.86 ( 516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8179 (mm-30) REVERT: A 88 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8309 (mmtm) REVERT: A 156 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8384 (ptmm) REVERT: B 12 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7699 (mmm160) REVERT: B 52 LYS cc_start: 0.9395 (tttm) cc_final: 0.7050 (mppt) REVERT: B 116 LYS cc_start: 0.9093 (mttm) cc_final: 0.7330 (mtmt) REVERT: C 41 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.7908 (mtm180) REVERT: C 205 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8213 (mt-10) REVERT: D 42 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7866 (mttp) outliers start: 22 outliers final: 15 residues processed: 131 average time/residue: 0.5413 time to fit residues: 74.5337 Evaluate side-chains 132 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 50 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [51, 60, 73, 6, 4, 75, 1, 32, 53, 11, 42] chunk 51 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.089540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.074530 restraints weight = 10745.903| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.25 r_work: 0.2767 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6574 Z= 0.158 Angle : 0.512 8.568 8955 Z= 0.263 Chirality : 0.044 0.219 1009 Planarity : 0.004 0.027 1157 Dihedral : 4.703 29.426 895 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.68 % Allowed : 17.63 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.11 (0.28), residues: 811 helix: -1.50 (0.61), residues: 66 sheet: 0.75 (0.36), residues: 197 loop : 0.09 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.015 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.001 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 6574) covalent geometry : angle 0.51194 / 0.26 ( 8955) hydrogen bonds : bond 0.03068 / 2.11 ( 171) hydrogen bonds : angle 5.37182 / 3.79 ( 516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8220 (mm-30) REVERT: A 88 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8276 (mmtm) REVERT: A 156 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8331 (ptmm) REVERT: B 52 LYS cc_start: 0.9365 (tttm) cc_final: 0.7005 (mppt) REVERT: B 116 LYS cc_start: 0.9037 (mttm) cc_final: 0.7280 (mtmt) REVERT: C 79 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8525 (mm110) REVERT: C 205 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8193 (mt-10) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 0.5266 time to fit residues: 70.2968 Evaluate side-chains 131 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 50 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [21, 22, 36, 78, 35, 8, 17, 53, 33, 65, 41] chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.089549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.074409 restraints weight = 10952.049| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.27 r_work: 0.2765 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6574 Z= 0.169 Angle : 0.539 8.466 8955 Z= 0.278 Chirality : 0.044 0.213 1009 Planarity : 0.004 0.027 1157 Dihedral : 4.695 29.379 895 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.54 % Allowed : 18.05 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.09 (0.28), residues: 811 helix: -1.52 (0.60), residues: 66 sheet: 0.76 (0.36), residues: 197 loop : 0.07 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.011 0.001 TYR C 191 PHE 0.010 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 6574) covalent geometry : angle 0.53890 / 0.28 ( 8955) hydrogen bonds : bond 0.03095 / 2.12 ( 171) hydrogen bonds : angle 5.35872 / 3.78 ( 516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8220 (mm-30) REVERT: A 88 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8303 (mmtm) REVERT: A 156 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8381 (ptmm) REVERT: B 12 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7636 (mmm160) REVERT: B 52 LYS cc_start: 0.9387 (tttm) cc_final: 0.7032 (mppt) REVERT: B 116 LYS cc_start: 0.9080 (mttm) cc_final: 0.7330 (mtmt) REVERT: C 205 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8223 (mt-10) REVERT: C 237 GLU cc_start: 0.7932 (pm20) cc_final: 0.6913 (pp20) REVERT: D 42 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7894 (mttp) outliers start: 18 outliers final: 13 residues processed: 129 average time/residue: 0.5279 time to fit residues: 71.3959 Evaluate side-chains 131 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [76, 41, 19, 51, 60, 13, 78, 30, 2, 48, 34] chunk 76 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.089191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.074068 restraints weight = 10751.594| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.27 r_work: 0.2759 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6574 Z= 0.181 Angle : 0.532 8.474 8955 Z= 0.273 Chirality : 0.044 0.216 1009 Planarity : 0.004 0.027 1157 Dihedral : 4.728 29.409 895 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.26 % Allowed : 18.62 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.08 (0.28), residues: 811 helix: -1.52 (0.60), residues: 66 sheet: 0.75 (0.36), residues: 197 loop : 0.06 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.011 0.001 TYR D 32 PHE 0.010 0.001 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.002 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 6574) covalent geometry : angle 0.53234 / 0.27 ( 8955) hydrogen bonds : bond 0.03152 / 2.15 ( 171) hydrogen bonds : angle 5.38068 / 3.80 ( 516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8263 (mm-30) REVERT: A 88 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8289 (mmtm) REVERT: A 156 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8340 (ptmm) REVERT: B 12 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7930 (mmm160) REVERT: B 52 LYS cc_start: 0.9370 (tttm) cc_final: 0.7008 (mppt) REVERT: B 116 LYS cc_start: 0.9049 (mttm) cc_final: 0.7296 (mtmt) REVERT: C 205 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8208 (mt-10) REVERT: C 237 GLU cc_start: 0.7892 (pm20) cc_final: 0.6889 (pp20) REVERT: D 42 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7880 (mttp) outliers start: 16 outliers final: 13 residues processed: 126 average time/residue: 0.5275 time to fit residues: 69.7093 Evaluate side-chains 128 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [17, 65, 56, 47, 67, 38, 18, 9, 5, 52, 55] chunk 17 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.0870 overall best weight: 1.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 GLN C 101 ASN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.091251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.076249 restraints weight = 10712.145| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.27 r_work: 0.2801 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6574 Z= 0.112 Angle : 0.512 8.713 8955 Z= 0.264 Chirality : 0.043 0.197 1009 Planarity : 0.004 0.028 1157 Dihedral : 4.459 28.964 895 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.12 % Allowed : 18.76 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.14 (0.28), residues: 811 helix: -1.48 (0.61), residues: 66 sheet: 0.77 (0.36), residues: 198 loop : 0.12 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.008 0.001 TYR A 76 PHE 0.009 0.001 PHE C 215 TRP 0.007 0.001 TRP B 79 HIS 0.002 0.000 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6574) covalent geometry : angle 0.51165 / 0.26 ( 8955) hydrogen bonds : bond 0.02781 / 1.91 ( 171) hydrogen bonds : angle 5.13360 / 3.63 ( 516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.43 seconds wall clock time: 44 minutes 19.26 seconds (2659.26 seconds total)