Starting phenix.real_space_refine on Fri Sep 11 01:25:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4o_65640/09_2026/9w4o_65640.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4o_65640/09_2026/9w4o_65640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w4o_65640/09_2026/9w4o_65640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4o_65640/09_2026/9w4o_65640.map" model { file = "/net/cci-nas-00/data/ceres_data/9w4o_65640/09_2026/9w4o_65640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4o_65640/09_2026/9w4o_65640.cif" } resolution = 2.52 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= 0.004 sd= 0.092 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 41 5.16 5 C 4065 2.51 5 N 1087 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6398 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2299 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1880 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1901 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: 1.55, per 1000 atoms: 0.24 Number of scatterers: 6398 At special positions: 0 Unit cell: (98.115, 100.225, 84.4, 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 41 16.00 O 1205 8.00 N 1087 7.00 C 4065 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: 0.52 Conformation dependent library (CDL) restraints added in 368.1 milliseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1532 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 15.6% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 57 removed outlier: 3.538A pdb=" N THR A 57 " --> pdb=" O VAL A 54 " (cutoff:3.500A) No H-bonds generated for '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: 3.813A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.815A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 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 43 through 47 removed outlier: 3.605A pdb=" N ALA B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.798A pdb=" N ARG B 151 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.116A pdb=" N MET 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 35 through 39 Processing helix chain 'D' and resid 50 through 55 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: 6.584A pdb=" N VAL A 239 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 71 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 237 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 73 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 235 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU A 75 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 233 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA C 22 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.875A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.990A pdb=" N ALA A 169 " --> pdb=" O PHE A 147 " (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: 6.901A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.248A 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: 6.901A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.600A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.111A 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: 6.726A pdb=" N LEU C 80 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET C 196 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 82 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.711A 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: 6.255A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 513 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: 0.72 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: 2083 1.34 - 1.46: 1234 1.46 - 1.57: 3176 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 6561 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 4.63e+01 bond pdb=" C3 SPH A 301 " pdb=" O3 SPH A 301 " ideal model delta sigma weight residual 1.438 1.408 0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" N LYS A 242 " pdb=" CA LYS A 242 " ideal model delta sigma weight residual 1.463 1.447 0.016 1.22e-02 6.72e+03 1.63e+00 bond pdb=" C1 SPH A 301 " pdb=" O1 SPH A 301 " ideal model delta sigma weight residual 1.433 1.409 0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" C2 SPH A 301 " pdb=" C3 SPH A 301 " ideal model delta sigma weight residual 1.544 1.524 0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 6556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 8839 2.06 - 4.12: 92 4.12 - 6.18: 4 6.18 - 8.24: 1 8.24 - 10.30: 1 Bond angle restraints: 8937 Sorted by residual: angle pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " pdb=" C6 SPH A 301 " ideal model delta sigma weight residual 128.38 118.08 10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 112.98 109.46 3.52 1.25e+00 6.40e-01 7.93e+00 angle pdb=" CA LEU A 208 " pdb=" CB LEU A 208 " pdb=" CG LEU A 208 " ideal model delta sigma weight residual 116.30 124.25 -7.95 3.50e+00 8.16e-02 5.16e+00 angle pdb=" CG1 VAL A 23 " pdb=" CB VAL A 23 " pdb=" CG2 VAL A 23 " ideal model delta sigma weight residual 110.80 105.99 4.81 2.20e+00 2.07e-01 4.79e+00 angle pdb=" C PRO B 56 " pdb=" N GLU B 57 " pdb=" CA GLU B 57 " ideal model delta sigma weight residual 121.54 125.22 -3.68 1.91e+00 2.74e-01 3.72e+00 ... (remaining 8932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3433 17.73 - 35.46: 346 35.46 - 53.19: 88 53.19 - 70.91: 26 70.91 - 88.64: 7 Dihedral angle restraints: 3900 sinusoidal: 1526 harmonic: 2374 Sorted by residual: dihedral pdb=" CA ASP D 35 " pdb=" CB ASP D 35 " pdb=" CG ASP D 35 " pdb=" OD1 ASP D 35 " ideal model delta sinusoidal sigma weight residual -30.00 -86.42 56.42 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CB GLU A 15 " pdb=" CG GLU A 15 " pdb=" CD GLU A 15 " pdb=" OE1 GLU A 15 " ideal model delta sinusoidal sigma weight residual 0.00 88.64 -88.64 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CG ARG B 67 " pdb=" CD ARG B 67 " pdb=" NE ARG B 67 " pdb=" CZ ARG B 67 " ideal model delta sinusoidal sigma weight residual -180.00 -136.89 -43.11 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 3897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 739 0.043 - 0.086: 194 0.086 - 0.129: 68 0.129 - 0.172: 1 0.172 - 0.216: 2 Chirality restraints: 1004 Sorted by residual: chirality pdb=" C3 SPH A 301 " pdb=" C2 SPH A 301 " pdb=" C4 SPH A 301 " pdb=" O3 SPH A 301 " both_signs ideal model delta sigma weight residual False 2.42 2.21 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE A 211 " pdb=" CA ILE A 211 " pdb=" CG1 ILE A 211 " pdb=" CG2 ILE A 211 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1001 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH A 301 " -0.020 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C4 SPH A 301 " 0.021 2.00e-02 2.50e+03 pdb=" C5 SPH A 301 " 0.017 2.00e-02 2.50e+03 pdb=" C6 SPH A 301 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 148 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 149 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 229 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 230 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.015 5.00e-02 4.00e+02 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 3680 3.03 - 3.50: 6050 3.50 - 3.97: 10961 3.97 - 4.43: 13129 4.43 - 4.90: 20404 Nonbonded interactions: 54224 Sorted by model distance: nonbonded pdb=" N ASP C 208 " pdb=" OD1 ASP C 208 " model vdw 2.567 3.120 nonbonded pdb=" OD1 ASP B 51 " pdb=" OD1 ASN B 240 " model vdw 2.576 3.040 nonbonded pdb=" N2 SPH A 301 " pdb=" O1 SPH A 301 " model vdw 2.583 2.496 nonbonded pdb=" N VAL A 29 " pdb=" N GLU A 30 " model vdw 2.616 2.560 nonbonded pdb=" OG1 THR B 171 " pdb=" O GLU C 50 " model vdw 2.619 3.040 ... (remaining 54219 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: 0.590 Set stop_for_unknowns flag: 0.010 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: 7.370 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 6561 Z= 0.176 Angle : 0.529 10.303 8937 Z= 0.270 Chirality : 0.043 0.216 1004 Planarity : 0.004 0.031 1156 Dihedral : 16.220 88.643 2368 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.97 % Allowed : 18.41 % Favored : 78.61 % 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: -0.42 (0.28), residues: 812 helix: -1.80 (0.61), residues: 66 sheet: 0.44 (0.38), residues: 197 loop : -0.32 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.014 0.001 TYR B 31 PHE 0.008 0.001 PHE C 117 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 6561) covalent geometry : angle 0.52895 / 0.27 ( 8937) hydrogen bonds : bond 0.18802 / 11.65 ( 173) hydrogen bonds : angle 8.21102 / 5.67 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8824 (ttpp) cc_final: 0.8547 (ttpt) REVERT: A 19 GLU cc_start: 0.7997 (pm20) cc_final: 0.7245 (pp20) REVERT: A 102 GLN cc_start: 0.8689 (mm110) cc_final: 0.8372 (tp40) REVERT: A 136 MET cc_start: 0.5445 (ttt) cc_final: 0.2923 (mmm) REVERT: A 161 PHE cc_start: 0.8361 (m-80) cc_final: 0.6910 (p90) REVERT: A 164 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: A 227 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8007 (tm-30) REVERT: B 185 SER cc_start: 0.9223 (t) cc_final: 0.9006 (m) REVERT: C 41 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7995 (mtm180) REVERT: C 114 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7781 (pp20) REVERT: C 124 MET cc_start: 0.8476 (mmm) cc_final: 0.8262 (mmp) REVERT: C 145 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: C 229 ASP cc_start: 0.8427 (m-30) cc_final: 0.7733 (m-30) outliers start: 21 outliers final: 17 residues processed: 121 average time/residue: 0.5352 time to fit residues: 68.1608 Evaluate side-chains 127 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 173 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 44 GLN A 292 HIS B 45 HIS B 55 GLN B 111 GLN B 206 GLN B 240 ASN C 235 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.090211 restraints weight = 7627.818| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.89 r_work: 0.2896 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6561 Z= 0.151 Angle : 0.496 5.819 8937 Z= 0.259 Chirality : 0.043 0.148 1004 Planarity : 0.004 0.029 1156 Dihedral : 8.059 59.372 936 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.26 % Allowed : 17.85 % Favored : 78.90 % 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: -0.26 (0.28), residues: 812 helix: -1.45 (0.65), residues: 60 sheet: 0.54 (0.38), residues: 197 loop : -0.25 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.015 0.001 TYR B 31 PHE 0.015 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 6561) covalent geometry : angle 0.49604 / 0.26 ( 8937) hydrogen bonds : bond 0.04041 / 2.53 ( 173) hydrogen bonds : angle 6.00809 / 4.19 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8571 (ttpt) REVERT: A 19 GLU cc_start: 0.8015 (pm20) cc_final: 0.7210 (mm-30) REVERT: A 98 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7911 (mttm) REVERT: A 136 MET cc_start: 0.5214 (ttt) cc_final: 0.2761 (mmm) REVERT: A 161 PHE cc_start: 0.8081 (m-80) cc_final: 0.5966 (p90) REVERT: A 164 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6329 (mp10) REVERT: A 227 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8031 (tm-30) REVERT: C 114 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7829 (pp20) REVERT: C 124 MET cc_start: 0.8502 (mmm) cc_final: 0.8297 (mmp) REVERT: C 145 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: C 229 ASP cc_start: 0.8462 (m-30) cc_final: 0.7743 (m-30) outliers start: 23 outliers final: 10 residues processed: 121 average time/residue: 0.5029 time to fit residues: 64.2502 Evaluate side-chains 114 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 0.0050 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 HIS ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 240 ASN C 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.092894 restraints weight = 7569.245| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.90 r_work: 0.2940 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6561 Z= 0.095 Angle : 0.452 6.461 8937 Z= 0.234 Chirality : 0.042 0.148 1004 Planarity : 0.004 0.028 1156 Dihedral : 7.299 57.653 918 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.97 % Allowed : 17.56 % Favored : 78.47 % 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: -0.21 (0.28), residues: 812 helix: -1.32 (0.66), residues: 60 sheet: 0.59 (0.36), residues: 213 loop : -0.26 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.014 0.001 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.005 0.001 TRP B 207 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 ( 6561) covalent geometry : angle 0.45168 / 0.23 ( 8937) hydrogen bonds : bond 0.03283 / 2.07 ( 173) hydrogen bonds : angle 5.58452 / 3.90 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8556 (ttpt) REVERT: A 136 MET cc_start: 0.5155 (ttt) cc_final: 0.2782 (mmm) REVERT: A 161 PHE cc_start: 0.8041 (m-80) cc_final: 0.6846 (p90) REVERT: A 227 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8026 (tm-30) REVERT: C 114 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7999 (pp20) REVERT: C 124 MET cc_start: 0.8465 (mmm) cc_final: 0.8218 (mmp) REVERT: C 229 ASP cc_start: 0.8452 (m-30) cc_final: 0.7754 (m-30) outliers start: 28 outliers final: 11 residues processed: 127 average time/residue: 0.4645 time to fit residues: 62.2245 Evaluate side-chains 115 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.087741 restraints weight = 7871.848| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.89 r_work: 0.2873 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6561 Z= 0.221 Angle : 0.538 6.618 8937 Z= 0.279 Chirality : 0.045 0.143 1004 Planarity : 0.004 0.032 1156 Dihedral : 7.347 57.157 909 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.11 % Allowed : 17.28 % Favored : 78.61 % 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: -0.34 (0.28), residues: 812 helix: -1.55 (0.61), residues: 66 sheet: 0.54 (0.38), residues: 197 loop : -0.31 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 104 TYR 0.018 0.002 TYR B 31 PHE 0.020 0.002 PHE C 123 TRP 0.009 0.001 TRP B 177 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 ( 6561) covalent geometry : angle 0.53785 / 0.28 ( 8937) hydrogen bonds : bond 0.03993 / 2.54 ( 173) hydrogen bonds : angle 5.67206 / 3.97 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8590 (ttpt) REVERT: A 98 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7953 (mttm) REVERT: A 136 MET cc_start: 0.5341 (ttt) cc_final: 0.2745 (mmm) REVERT: A 161 PHE cc_start: 0.8117 (m-80) cc_final: 0.6868 (p90) REVERT: A 227 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8002 (tm-30) REVERT: A 277 LEU cc_start: 0.8928 (tp) cc_final: 0.8725 (mt) REVERT: C 114 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7984 (pp20) REVERT: C 145 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: C 229 ASP cc_start: 0.8498 (m-30) cc_final: 0.7779 (m-30) REVERT: D 43 LYS cc_start: 0.7698 (mttp) cc_final: 0.5528 (ttpt) outliers start: 29 outliers final: 14 residues processed: 122 average time/residue: 0.4866 time to fit residues: 62.6059 Evaluate side-chains 114 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.088211 restraints weight = 7798.009| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.92 r_work: 0.2866 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6561 Z= 0.220 Angle : 0.544 6.842 8937 Z= 0.281 Chirality : 0.045 0.147 1004 Planarity : 0.004 0.031 1156 Dihedral : 7.410 56.620 909 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.11 % Allowed : 16.71 % Favored : 79.18 % 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: -0.38 (0.28), residues: 812 helix: -1.58 (0.60), residues: 66 sheet: 0.52 (0.38), residues: 197 loop : -0.35 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 228 TYR 0.017 0.002 TYR B 31 PHE 0.016 0.002 PHE C 123 TRP 0.009 0.001 TRP B 177 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 ( 6561) covalent geometry : angle 0.54352 / 0.28 ( 8937) hydrogen bonds : bond 0.03952 / 2.51 ( 173) hydrogen bonds : angle 5.64257 / 3.95 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8581 (ttpt) REVERT: A 65 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.5980 (mmm160) REVERT: A 136 MET cc_start: 0.5402 (ttt) cc_final: 0.2819 (mmm) REVERT: A 161 PHE cc_start: 0.8098 (m-80) cc_final: 0.6866 (p90) REVERT: A 227 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7994 (tm-30) REVERT: A 277 LEU cc_start: 0.8925 (tp) cc_final: 0.8722 (mt) REVERT: C 114 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7877 (pp20) REVERT: C 145 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: C 229 ASP cc_start: 0.8481 (m-30) cc_final: 0.7774 (m-30) REVERT: D 43 LYS cc_start: 0.7684 (mttp) cc_final: 0.5538 (ttpt) outliers start: 29 outliers final: 18 residues processed: 121 average time/residue: 0.4838 time to fit residues: 61.7869 Evaluate side-chains 119 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 65 ARG Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 179 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 ASN C 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.091576 restraints weight = 7688.281| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.90 r_work: 0.2919 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6561 Z= 0.104 Angle : 0.466 6.834 8937 Z= 0.241 Chirality : 0.042 0.148 1004 Planarity : 0.004 0.029 1156 Dihedral : 7.071 59.260 909 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.68 % Allowed : 17.28 % Favored : 79.04 % 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: -0.25 (0.28), residues: 812 helix: -1.38 (0.64), residues: 60 sheet: 0.56 (0.37), residues: 207 loop : -0.27 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.013 0.001 TYR B 31 PHE 0.013 0.001 PHE C 123 TRP 0.005 0.001 TRP B 207 HIS 0.002 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 6561) covalent geometry : angle 0.46562 / 0.24 ( 8937) hydrogen bonds : bond 0.03161 / 2.01 ( 173) hydrogen bonds : angle 5.39163 / 3.77 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8540 (ttpt) REVERT: A 136 MET cc_start: 0.5382 (ttt) cc_final: 0.2949 (mmm) REVERT: A 161 PHE cc_start: 0.8085 (m-80) cc_final: 0.6875 (p90) REVERT: A 227 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8022 (tm-30) REVERT: C 114 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: C 145 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: C 229 ASP cc_start: 0.8453 (m-30) cc_final: 0.7746 (m-30) REVERT: D 43 LYS cc_start: 0.7710 (mttp) cc_final: 0.5526 (ttpt) outliers start: 26 outliers final: 16 residues processed: 123 average time/residue: 0.4714 time to fit residues: 61.1681 Evaluate side-chains 120 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 ASN C 96 ASN C 101 ASN C 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.091132 restraints weight = 7657.001| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.89 r_work: 0.2915 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6561 Z= 0.121 Angle : 0.481 7.768 8937 Z= 0.247 Chirality : 0.042 0.148 1004 Planarity : 0.004 0.028 1156 Dihedral : 7.078 59.907 909 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.68 % Allowed : 17.00 % Favored : 79.32 % 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: -0.22 (0.28), residues: 812 helix: -1.31 (0.64), residues: 60 sheet: 0.57 (0.37), residues: 207 loop : -0.25 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.015 0.001 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6561) covalent geometry : angle 0.48079 / 0.25 ( 8937) hydrogen bonds : bond 0.03250 / 2.08 ( 173) hydrogen bonds : angle 5.32719 / 3.73 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8549 (ttpt) REVERT: A 136 MET cc_start: 0.5222 (ttt) cc_final: 0.2800 (mmm) REVERT: A 161 PHE cc_start: 0.8105 (m-80) cc_final: 0.6970 (p90) REVERT: A 227 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8030 (tm-30) REVERT: C 114 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7833 (pp20) REVERT: C 145 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: C 229 ASP cc_start: 0.8460 (m-30) cc_final: 0.7751 (m-30) REVERT: D 43 LYS cc_start: 0.7713 (mttp) cc_final: 0.5527 (ttpt) outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 0.4313 time to fit residues: 55.1686 Evaluate side-chains 120 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 ASN C 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.091934 restraints weight = 7655.052| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.90 r_work: 0.2924 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6561 Z= 0.104 Angle : 0.469 7.800 8937 Z= 0.242 Chirality : 0.042 0.148 1004 Planarity : 0.004 0.028 1156 Dihedral : 7.031 59.414 909 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.68 % Allowed : 17.14 % Favored : 79.18 % 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: -0.22 (0.28), residues: 812 helix: -1.25 (0.64), residues: 60 sheet: 0.50 (0.36), residues: 213 loop : -0.24 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.014 0.001 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 6561) covalent geometry : angle 0.46873 / 0.24 ( 8937) hydrogen bonds : bond 0.03105 / 1.98 ( 173) hydrogen bonds : angle 5.27190 / 3.69 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8539 (ttpt) REVERT: A 136 MET cc_start: 0.5350 (ttt) cc_final: 0.2889 (mmm) REVERT: A 161 PHE cc_start: 0.8110 (m-80) cc_final: 0.6878 (p90) REVERT: A 227 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8029 (tm-30) REVERT: C 114 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7833 (pp20) REVERT: C 145 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: C 229 ASP cc_start: 0.8469 (m-30) cc_final: 0.7756 (m-30) REVERT: D 43 LYS cc_start: 0.7708 (mttp) cc_final: 0.5531 (ttpt) outliers start: 26 outliers final: 17 residues processed: 120 average time/residue: 0.4701 time to fit residues: 59.6549 Evaluate side-chains 121 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.092087 restraints weight = 7773.309| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.90 r_work: 0.2927 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6561 Z= 0.109 Angle : 0.476 8.063 8937 Z= 0.244 Chirality : 0.042 0.147 1004 Planarity : 0.004 0.029 1156 Dihedral : 7.030 59.439 909 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.12 % Allowed : 18.13 % Favored : 78.75 % 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: -0.20 (0.28), residues: 812 helix: -1.23 (0.65), residues: 60 sheet: 0.51 (0.36), residues: 213 loop : -0.22 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.015 0.001 TYR B 31 PHE 0.020 0.001 PHE C 123 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6561) covalent geometry : angle 0.47635 / 0.24 ( 8937) hydrogen bonds : bond 0.03128 / 2.00 ( 173) hydrogen bonds : angle 5.25643 / 3.68 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8542 (ttpt) REVERT: A 136 MET cc_start: 0.5345 (ttt) cc_final: 0.2887 (mmm) REVERT: A 161 PHE cc_start: 0.8062 (m-80) cc_final: 0.7044 (p90) REVERT: A 227 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8029 (tm-30) REVERT: C 114 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7858 (pp20) REVERT: C 145 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: C 227 MET cc_start: 0.9223 (ttm) cc_final: 0.9010 (ttp) REVERT: C 229 ASP cc_start: 0.8456 (m-30) cc_final: 0.7753 (m-30) REVERT: D 43 LYS cc_start: 0.7716 (mttp) cc_final: 0.5526 (ttpt) outliers start: 22 outliers final: 15 residues processed: 117 average time/residue: 0.4716 time to fit residues: 58.3665 Evaluate side-chains 116 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 8.9990 chunk 53 optimal weight: 0.0870 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.088823 restraints weight = 7682.951| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.89 r_work: 0.2880 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6561 Z= 0.214 Angle : 0.552 8.363 8937 Z= 0.283 Chirality : 0.045 0.158 1004 Planarity : 0.004 0.030 1156 Dihedral : 7.405 55.508 909 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.97 % Allowed : 18.27 % Favored : 78.75 % 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: -0.27 (0.28), residues: 812 helix: -1.33 (0.62), residues: 66 sheet: 0.55 (0.38), residues: 197 loop : -0.27 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 104 TYR 0.018 0.002 TYR B 31 PHE 0.023 0.002 PHE C 123 TRP 0.008 0.001 TRP B 177 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 ( 6561) covalent geometry : angle 0.55173 / 0.28 ( 8937) hydrogen bonds : bond 0.03811 / 2.44 ( 173) hydrogen bonds : angle 5.47454 / 3.84 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8616 (ttpt) REVERT: A 136 MET cc_start: 0.5483 (ttt) cc_final: 0.2913 (mmm) REVERT: A 161 PHE cc_start: 0.8155 (m-80) cc_final: 0.7012 (p90) REVERT: A 227 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8042 (tt0) REVERT: A 277 LEU cc_start: 0.8939 (tp) cc_final: 0.8724 (mt) REVERT: C 114 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8121 (pp20) REVERT: C 145 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: C 227 MET cc_start: 0.9245 (ttm) cc_final: 0.9038 (ttp) REVERT: C 229 ASP cc_start: 0.8469 (m-30) cc_final: 0.7773 (m-30) REVERT: D 43 LYS cc_start: 0.7715 (mttp) cc_final: 0.5569 (ttpt) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.4839 time to fit residues: 59.3275 Evaluate side-chains 118 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 240 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 = 0.3256 r_free = 0.3256 target = 0.109876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.089729 restraints weight = 7741.869| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.92 r_work: 0.2893 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6561 Z= 0.136 Angle : 0.515 8.307 8937 Z= 0.264 Chirality : 0.044 0.222 1004 Planarity : 0.004 0.029 1156 Dihedral : 7.305 57.558 909 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.54 % Allowed : 17.85 % Favored : 78.61 % 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: -0.21 (0.28), residues: 812 helix: -1.15 (0.65), residues: 60 sheet: 0.53 (0.38), residues: 197 loop : -0.24 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.016 0.001 TYR B 31 PHE 0.027 0.001 PHE C 123 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6561) covalent geometry : angle 0.51510 / 0.26 ( 8937) hydrogen bonds : bond 0.03466 / 2.24 ( 173) hydrogen bonds : angle 5.40729 / 3.79 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.47 seconds wall clock time: 43 minutes 28.74 seconds (2608.74 seconds total)