Starting phenix.real_space_refine on Fri Sep 11 13:13:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e40_27875/09_2026/8e40_27875.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e40_27875/09_2026/8e40_27875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e40_27875/09_2026/8e40_27875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e40_27875/09_2026/8e40_27875.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8e40_27875/09_2026/8e40_27875.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e40_27875/09_2026/8e40_27875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e40_27875/09_2026/8e40_27875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e40_27875/09_2026/8e40_27875.map" } resolution = 3.57 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3868 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 47 5.49 5 S 30 5.16 5 C 3835 2.51 5 N 1122 2.21 5 O 1261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6297 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3085 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 347} Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1000 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain: "R" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'RNAv2': 22} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 14} Link IDs: {'rna3p': 21} Chain: "r" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 534 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 21} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 757 SG CYS A 97 34.707 53.781 84.146 1.00 27.23 S ATOM 781 SG CYS A 100 30.843 53.501 86.010 1.00 32.88 S ATOM 2300 SG CYS A 287 59.635 23.728 72.488 1.00 60.84 S Time building chain proxies: 1.48, per 1000 atoms: 0.24 Number of scatterers: 6297 At special positions: 0 Unit cell: (92.92, 98.44, 134.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 30 16.00 P 47 15.00 O 1261 8.00 N 1122 7.00 C 3835 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: 0.41 Conformation dependent library (CDL) restraints added in 241.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 65 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 100 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 287 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 257 " 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 38.5% alpha, 16.7% beta 17 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 65 through 79 Processing helix chain 'A' and resid 97 through 111 removed outlier: 4.056A pdb=" N THR A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.851A pdb=" N ALA A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 removed outlier: 3.825A pdb=" N VAL A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.962A pdb=" N THR A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.890A pdb=" N LEU A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.758A pdb=" N MET A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 removed outlier: 4.049A pdb=" N GLY A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 362 through 379 Processing helix chain 'B' and resid 14 through 31 Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 15 through 22 removed outlier: 3.866A pdb=" N ARG C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 70 through 75 removed outlier: 4.295A pdb=" N GLN C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.916A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 149 removed outlier: 3.677A pdb=" N ARG C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.767A pdb=" N TYR A 86 " --> pdb=" O THR A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 240 removed outlier: 5.035A pdb=" N VAL A 224 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N GLN A 237 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N TYR A 222 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG A 277 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 276 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N CYS A 307 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A 278 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE A 309 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A 280 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA A 335 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 308 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.492A pdb=" N THR B 68 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 65 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE B 87 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE B 9 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N TRP B 89 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 14.398A pdb=" N VAL B 7 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 55 " --> pdb=" O PHE C 68 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1818 1.34 - 1.46: 1791 1.46 - 1.58: 2826 1.58 - 1.70: 92 1.70 - 1.82: 43 Bond restraints: 6570 Sorted by residual: bond pdb=" N LEU C 119 " pdb=" CA LEU C 119 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.18e+00 bond pdb=" N ASP C 34 " pdb=" CA ASP C 34 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.35e-02 5.49e+03 6.11e+00 bond pdb=" C VAL C 5 " pdb=" N PRO C 6 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.08e+00 bond pdb=" N ASP C 120 " pdb=" CA ASP C 120 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.82e+00 bond pdb=" N ARG C 118 " pdb=" CA ARG C 118 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.33e-02 5.65e+03 4.32e+00 ... (remaining 6565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8600 2.02 - 4.05: 426 4.05 - 6.07: 63 6.07 - 8.09: 15 8.09 - 10.12: 7 Bond angle restraints: 9111 Sorted by residual: angle pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " pdb=" CG LYS A 113 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" C3' U r 2 " pdb=" O3' U r 2 " pdb=" P U r 3 " ideal model delta sigma weight residual 119.70 125.66 -5.96 1.20e+00 6.94e-01 2.47e+01 angle pdb=" CA GLU C 38 " pdb=" CB GLU C 38 " pdb=" CG GLU C 38 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" CA GLU A 302 " pdb=" CB GLU A 302 " pdb=" CG GLU A 302 " ideal model delta sigma weight residual 114.10 123.07 -8.97 2.00e+00 2.50e-01 2.01e+01 angle pdb=" N LEU A 260 " pdb=" CA LEU A 260 " pdb=" C LEU A 260 " ideal model delta sigma weight residual 111.36 106.48 4.88 1.09e+00 8.42e-01 2.01e+01 ... (remaining 9106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 3360 26.56 - 53.11: 364 53.11 - 79.67: 59 79.67 - 106.23: 3 106.23 - 132.79: 1 Dihedral angle restraints: 3787 sinusoidal: 1925 harmonic: 1862 Sorted by residual: dihedral pdb=" C4' A r 20 " pdb=" C3' A r 20 " pdb=" C2' A r 20 " pdb=" C1' A r 20 " ideal model delta sinusoidal sigma weight residual 36.34 -35.98 72.32 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' A r 17 " pdb=" C3' A r 17 " pdb=" C2' A r 17 " pdb=" C1' A r 17 " ideal model delta sinusoidal sigma weight residual 36.34 -35.11 71.46 1 3.10e+00 1.04e-01 6.81e+02 dihedral pdb=" C4' A r 16 " pdb=" C3' A r 16 " pdb=" C2' A r 16 " pdb=" C1' A r 16 " ideal model delta sinusoidal sigma weight residual 36.34 -33.28 69.63 1 3.10e+00 1.04e-01 6.51e+02 ... (remaining 3784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 796 0.072 - 0.143: 114 0.143 - 0.215: 14 0.215 - 0.286: 51 0.286 - 0.358: 3 Chirality restraints: 978 Sorted by residual: chirality pdb=" P A r 19 " pdb=" OP1 A r 19 " pdb=" OP2 A r 19 " pdb=" O5' A r 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C3' U r 2 " pdb=" C4' U r 2 " pdb=" O3' U r 2 " pdb=" C2' U r 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.14 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" P U R 21 " pdb=" OP1 U R 21 " pdb=" OP2 U R 21 " pdb=" O5' U R 21 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 975 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 13 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A 14 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 198 " 0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 199 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.053 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 234 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.044 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 837 2.76 - 3.29: 5650 3.29 - 3.83: 11067 3.83 - 4.36: 12501 4.36 - 4.90: 20514 Nonbonded interactions: 50569 Sorted by model distance: nonbonded pdb=" CB ALA A 258 " pdb=" SG CYS A 290 " model vdw 2.225 3.820 nonbonded pdb=" O ASP A 31 " pdb=" CG1 VAL A 58 " model vdw 2.235 3.460 nonbonded pdb=" N TYR A 59 " pdb=" CD PRO A 60 " model vdw 2.278 3.520 nonbonded pdb=" O PHE A 268 " pdb=" N6 A r 17 " model vdw 2.304 3.120 nonbonded pdb=" N GLN A 259 " pdb=" OE1 GLN A 259 " model vdw 2.316 3.120 ... (remaining 50564 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 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 : 0.009 0.585 6575 Z= 0.356 Angle : 0.994 10.118 9111 Z= 0.522 Chirality : 0.076 0.358 978 Planarity : 0.008 0.118 1008 Dihedral : 19.512 132.785 2581 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 2.12 % Allowed : 27.43 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.84 (0.30), residues: 626 helix: -1.56 (0.30), residues: 205 sheet: -1.40 (0.55), residues: 109 loop : -2.27 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 24 TYR 0.018 0.002 TYR A 219 PHE 0.034 0.002 PHE C 12 TRP 0.028 0.002 TRP A 211 HIS 0.007 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 ( 6570) covalent geometry : angle 0.99392 / 0.52 ( 9111) hydrogen bonds : bond 0.14650 / 9.49 ( 238) hydrogen bonds : angle 7.55533 / 5.20 ( 653) metal coordination : bond 0.28053 / 10.83 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7123 (t0) outliers start: 12 outliers final: 4 residues processed: 114 average time/residue: 0.0976 time to fit residues: 14.1424 Evaluate side-chains 59 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.079000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.059858 restraints weight = 35003.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.061640 restraints weight = 18794.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.062751 restraints weight = 13238.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.063433 restraints weight = 10770.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.063830 restraints weight = 9498.456| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 6575 Z= 0.297 Angle : 0.926 14.366 9111 Z= 0.435 Chirality : 0.054 0.383 978 Planarity : 0.006 0.061 1008 Dihedral : 12.242 134.832 1275 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.84 % Allowed : 27.61 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.07 (0.33), residues: 626 helix: -0.41 (0.34), residues: 218 sheet: -1.92 (0.47), residues: 129 loop : -1.78 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 15 TYR 0.022 0.002 TYR A 91 PHE 0.020 0.003 PHE A 241 TRP 0.021 0.002 TRP B 70 HIS 0.007 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.30 ( 6570) covalent geometry : angle 0.92563 / 0.44 ( 9111) hydrogen bonds : bond 0.06132 / 4.09 ( 238) hydrogen bonds : angle 5.74601 / 3.86 ( 653) metal coordination : bond 0.01307 / 0.67 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TRP cc_start: 0.8198 (t60) cc_final: 0.7844 (t-100) REVERT: A 86 TYR cc_start: 0.8004 (m-10) cc_final: 0.7647 (m-10) REVERT: A 197 MET cc_start: 0.8760 (ppp) cc_final: 0.8390 (ppp) REVERT: B 37 ASP cc_start: 0.7836 (t0) cc_final: 0.7514 (t0) REVERT: B 39 PHE cc_start: 0.8608 (m-80) cc_final: 0.8338 (m-80) REVERT: B 54 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8290 (tt0) REVERT: C 13 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9070 (pp20) outliers start: 33 outliers final: 17 residues processed: 83 average time/residue: 0.0817 time to fit residues: 9.0062 Evaluate side-chains 68 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS ** A 301 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 = 0.4148 r_free = 0.4148 target = 0.080468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.061733 restraints weight = 34476.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.063542 restraints weight = 18304.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064697 restraints weight = 12889.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.065395 restraints weight = 10447.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.065828 restraints weight = 9184.529| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.245 6575 Z= 0.534 Angle : 0.721 8.996 9111 Z= 0.332 Chirality : 0.051 0.330 978 Planarity : 0.005 0.042 1008 Dihedral : 11.847 131.465 1267 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.78 % Allowed : 26.19 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.34), residues: 626 helix: 0.00 (0.35), residues: 214 sheet: -1.90 (0.45), residues: 139 loop : -1.46 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 375 TYR 0.010 0.001 TYR A 339 PHE 0.017 0.002 PHE A 164 TRP 0.012 0.001 TRP B 70 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6570) covalent geometry : angle 0.72072 / 0.33 ( 9111) hydrogen bonds : bond 0.03953 / 2.69 ( 238) hydrogen bonds : angle 5.18703 / 3.46 ( 653) metal coordination : bond 0.55669 / 27.83 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8332 (ptmm) REVERT: A 86 TYR cc_start: 0.7645 (m-10) cc_final: 0.7322 (m-10) REVERT: A 197 MET cc_start: 0.8683 (ppp) cc_final: 0.8366 (ppp) REVERT: A 371 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8965 (p) REVERT: B 37 ASP cc_start: 0.7667 (t0) cc_final: 0.7447 (t0) REVERT: B 39 PHE cc_start: 0.8679 (m-80) cc_final: 0.8437 (m-80) REVERT: B 54 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8214 (tt0) REVERT: C 67 GLN cc_start: 0.8742 (tp40) cc_final: 0.8406 (mm-40) outliers start: 27 outliers final: 17 residues processed: 79 average time/residue: 0.0816 time to fit residues: 8.6368 Evaluate side-chains 69 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.079862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.060892 restraints weight = 34566.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.062717 restraints weight = 18561.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.063823 restraints weight = 13140.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.064529 restraints weight = 10751.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.064925 restraints weight = 9513.872| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6575 Z= 0.171 Angle : 0.735 9.650 9111 Z= 0.337 Chirality : 0.050 0.316 978 Planarity : 0.004 0.053 1008 Dihedral : 11.828 131.190 1265 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.84 % Allowed : 25.13 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.34), residues: 626 helix: 0.14 (0.35), residues: 214 sheet: -1.93 (0.44), residues: 141 loop : -1.39 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.010 0.001 TYR A 91 PHE 0.017 0.002 PHE A 164 TRP 0.012 0.001 TRP A 77 HIS 0.051 0.002 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 6570) covalent geometry : angle 0.73523 / 0.34 ( 9111) hydrogen bonds : bond 0.04358 / 2.95 ( 238) hydrogen bonds : angle 5.05219 / 3.35 ( 653) metal coordination : bond 0.03551 / 1.99 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8310 (ptmm) REVERT: A 86 TYR cc_start: 0.7674 (m-10) cc_final: 0.7457 (m-10) REVERT: A 197 MET cc_start: 0.8706 (ppp) cc_final: 0.8331 (ppp) REVERT: B 37 ASP cc_start: 0.7746 (t0) cc_final: 0.7487 (t0) REVERT: B 39 PHE cc_start: 0.8648 (m-80) cc_final: 0.8367 (m-80) REVERT: B 54 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8199 (tt0) REVERT: C 39 GLU cc_start: 0.8677 (tp30) cc_final: 0.8286 (tt0) REVERT: C 67 GLN cc_start: 0.8812 (tp40) cc_final: 0.8487 (mm-40) outliers start: 33 outliers final: 21 residues processed: 87 average time/residue: 0.0782 time to fit residues: 9.1543 Evaluate side-chains 75 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 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 = 0.4147 r_free = 0.4147 target = 0.080273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.061373 restraints weight = 34932.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.063185 restraints weight = 18715.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.064349 restraints weight = 13220.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.065055 restraints weight = 10728.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.065356 restraints weight = 9462.259| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6575 Z= 0.141 Angle : 0.691 7.744 9111 Z= 0.313 Chirality : 0.049 0.326 978 Planarity : 0.004 0.034 1008 Dihedral : 11.729 129.480 1265 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.37 % Allowed : 23.01 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.34), residues: 626 helix: 0.42 (0.35), residues: 213 sheet: -1.77 (0.45), residues: 141 loop : -1.31 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.008 0.001 TYR A 182 PHE 0.019 0.002 PHE C 12 TRP 0.018 0.001 TRP A 77 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 6570) covalent geometry : angle 0.69112 / 0.31 ( 9111) hydrogen bonds : bond 0.03903 / 2.66 ( 238) hydrogen bonds : angle 4.92503 / 3.24 ( 653) metal coordination : bond 0.01805 / 1.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: A 61 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8191 (ptmm) REVERT: A 77 TRP cc_start: 0.8100 (t-100) cc_final: 0.7270 (t60) REVERT: A 86 TYR cc_start: 0.7763 (m-10) cc_final: 0.6017 (m-10) REVERT: A 197 MET cc_start: 0.8763 (ppp) cc_final: 0.8343 (ppp) REVERT: B 37 ASP cc_start: 0.7846 (t0) cc_final: 0.7566 (t0) REVERT: B 54 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8226 (tt0) REVERT: C 13 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9079 (pp20) REVERT: C 39 GLU cc_start: 0.8810 (tp30) cc_final: 0.8495 (tt0) REVERT: C 67 GLN cc_start: 0.8851 (tp40) cc_final: 0.8529 (mm-40) outliers start: 36 outliers final: 24 residues processed: 86 average time/residue: 0.0685 time to fit residues: 7.8526 Evaluate side-chains 79 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** 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 = 0.4121 r_free = 0.4121 target = 0.078896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.060040 restraints weight = 34603.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.061822 restraints weight = 18725.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.062927 restraints weight = 13315.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.063614 restraints weight = 10874.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.064056 restraints weight = 9623.838| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6575 Z= 0.170 Angle : 0.723 10.215 9111 Z= 0.325 Chirality : 0.049 0.318 978 Planarity : 0.004 0.030 1008 Dihedral : 11.754 128.896 1265 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.49 % Allowed : 25.13 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.34), residues: 626 helix: 0.44 (0.35), residues: 215 sheet: -1.77 (0.44), residues: 142 loop : -1.35 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.010 0.001 TYR A 91 PHE 0.018 0.002 PHE C 12 TRP 0.008 0.001 TRP A 77 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 6570) covalent geometry : angle 0.72304 / 0.32 ( 9111) hydrogen bonds : bond 0.04394 / 2.95 ( 238) hydrogen bonds : angle 5.02804 / 3.31 ( 653) metal coordination : bond 0.01963 / 1.19 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: A 61 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8134 (ptmm) REVERT: A 197 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8349 (ppp) REVERT: B 37 ASP cc_start: 0.7802 (t0) cc_final: 0.7530 (t0) REVERT: B 54 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8209 (tt0) REVERT: C 13 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9085 (pp20) REVERT: C 39 GLU cc_start: 0.8729 (tp30) cc_final: 0.8482 (tt0) outliers start: 31 outliers final: 26 residues processed: 78 average time/residue: 0.0739 time to fit residues: 7.8396 Evaluate side-chains 77 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.078860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.060031 restraints weight = 34503.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.061848 restraints weight = 18702.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.062959 restraints weight = 13228.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.063628 restraints weight = 10805.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.063807 restraints weight = 9559.577| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6575 Z= 0.156 Angle : 0.717 12.522 9111 Z= 0.319 Chirality : 0.049 0.327 978 Planarity : 0.004 0.029 1008 Dihedral : 11.768 126.921 1265 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.96 % Allowed : 26.37 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.34), residues: 626 helix: 0.49 (0.35), residues: 221 sheet: -1.71 (0.45), residues: 142 loop : -1.32 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.010 0.001 TYR C 29 PHE 0.018 0.002 PHE C 12 TRP 0.011 0.001 TRP A 77 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 6570) covalent geometry : angle 0.71685 / 0.32 ( 9111) hydrogen bonds : bond 0.04098 / 2.75 ( 238) hydrogen bonds : angle 4.96609 / 3.24 ( 653) metal coordination : bond 0.01099 / 0.63 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: A 138 LEU cc_start: 0.9475 (tp) cc_final: 0.9244 (tt) REVERT: A 197 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8347 (ppp) REVERT: B 37 ASP cc_start: 0.7789 (t0) cc_final: 0.7500 (t0) REVERT: B 54 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8206 (tt0) REVERT: C 13 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9123 (pp20) REVERT: C 39 GLU cc_start: 0.8813 (tp30) cc_final: 0.8579 (tt0) outliers start: 28 outliers final: 24 residues processed: 76 average time/residue: 0.0753 time to fit residues: 7.8978 Evaluate side-chains 75 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 61 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN A 303 HIS B 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.080256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.061635 restraints weight = 34400.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.063497 restraints weight = 18381.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.064653 restraints weight = 12948.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.065355 restraints weight = 10508.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.065797 restraints weight = 9265.917| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6575 Z= 0.122 Angle : 0.693 8.948 9111 Z= 0.308 Chirality : 0.048 0.330 978 Planarity : 0.003 0.028 1008 Dihedral : 11.684 125.033 1265 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.42 % Allowed : 26.90 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.35), residues: 626 helix: 0.54 (0.35), residues: 221 sheet: -1.54 (0.46), residues: 142 loop : -1.27 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.013 0.001 TYR A 86 PHE 0.017 0.001 PHE C 12 TRP 0.008 0.001 TRP A 77 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6570) covalent geometry : angle 0.69260 / 0.31 ( 9111) hydrogen bonds : bond 0.03746 / 2.53 ( 238) hydrogen bonds : angle 4.77419 / 3.09 ( 653) metal coordination : bond 0.00623 / 0.35 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: B 37 ASP cc_start: 0.7769 (t0) cc_final: 0.7523 (t0) REVERT: B 54 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8224 (tt0) REVERT: C 13 GLU cc_start: 0.9421 (mt-10) cc_final: 0.9081 (pp20) REVERT: C 67 GLN cc_start: 0.8922 (tp40) cc_final: 0.8592 (mm-40) outliers start: 25 outliers final: 19 residues processed: 75 average time/residue: 0.0797 time to fit residues: 8.2023 Evaluate side-chains 74 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 32 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 GLN C 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.080427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.061626 restraints weight = 34575.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.063494 restraints weight = 18536.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.064650 restraints weight = 13082.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.065322 restraints weight = 10630.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.065770 restraints weight = 9389.261| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6575 Z= 0.123 Angle : 0.709 11.897 9111 Z= 0.317 Chirality : 0.048 0.326 978 Planarity : 0.003 0.031 1008 Dihedral : 11.654 124.202 1265 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.25 % Allowed : 27.79 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.35), residues: 626 helix: 0.66 (0.36), residues: 217 sheet: -1.26 (0.48), residues: 133 loop : -1.14 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 40 TYR 0.008 0.001 TYR A 339 PHE 0.025 0.002 PHE C 44 TRP 0.007 0.001 TRP A 77 HIS 0.004 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6570) covalent geometry : angle 0.70929 / 0.32 ( 9111) hydrogen bonds : bond 0.03798 / 2.56 ( 238) hydrogen bonds : angle 4.78634 / 3.10 ( 653) metal coordination : bond 0.00640 / 0.36 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: B 37 ASP cc_start: 0.7795 (t0) cc_final: 0.7578 (t0) REVERT: B 54 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8197 (tt0) REVERT: C 67 GLN cc_start: 0.8931 (tp40) cc_final: 0.8606 (mm-40) outliers start: 24 outliers final: 20 residues processed: 79 average time/residue: 0.0872 time to fit residues: 9.1935 Evaluate side-chains 76 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.0010 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.080852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.062325 restraints weight = 33933.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.064122 restraints weight = 18146.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.065302 restraints weight = 12838.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.066018 restraints weight = 10404.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.066368 restraints weight = 9177.708| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6575 Z= 0.120 Angle : 0.707 9.643 9111 Z= 0.317 Chirality : 0.048 0.328 978 Planarity : 0.003 0.027 1008 Dihedral : 11.629 123.316 1265 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.72 % Allowed : 27.61 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.35), residues: 626 helix: 0.76 (0.36), residues: 218 sheet: -1.39 (0.46), residues: 142 loop : -1.10 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.012 0.001 TYR A 86 PHE 0.019 0.002 PHE C 44 TRP 0.008 0.001 TRP C 113 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6570) covalent geometry : angle 0.70690 / 0.32 ( 9111) hydrogen bonds : bond 0.03684 / 2.49 ( 238) hydrogen bonds : angle 4.73378 / 3.07 ( 653) metal coordination : bond 0.00562 / 0.32 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ASP cc_start: 0.7846 (t0) cc_final: 0.7603 (t0) REVERT: B 54 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8202 (tt0) REVERT: B 83 GLN cc_start: 0.7834 (mt0) cc_final: 0.7529 (pt0) REVERT: B 113 ASP cc_start: 0.7554 (p0) cc_final: 0.7304 (m-30) REVERT: C 21 LEU cc_start: 0.7541 (tt) cc_final: 0.7331 (tp) outliers start: 21 outliers final: 18 residues processed: 74 average time/residue: 0.0863 time to fit residues: 8.6068 Evaluate side-chains 71 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.078392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.059609 restraints weight = 34312.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.061432 restraints weight = 18550.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.062542 restraints weight = 13132.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.063232 restraints weight = 10743.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.063625 restraints weight = 9497.094| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6575 Z= 0.192 Angle : 0.767 12.861 9111 Z= 0.347 Chirality : 0.048 0.317 978 Planarity : 0.004 0.029 1008 Dihedral : 11.813 124.096 1265 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.54 % Allowed : 27.79 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.35), residues: 626 helix: 0.87 (0.37), residues: 214 sheet: -1.37 (0.47), residues: 131 loop : -1.09 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 40 TYR 0.014 0.002 TYR A 91 PHE 0.023 0.002 PHE A 241 TRP 0.009 0.001 TRP B 5 HIS 0.004 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 6570) covalent geometry : angle 0.76675 / 0.35 ( 9111) hydrogen bonds : bond 0.04583 / 3.04 ( 238) hydrogen bonds : angle 5.00478 / 3.28 ( 653) metal coordination : bond 0.00941 / 0.53 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.87 seconds wall clock time: 26 minutes 47.46 seconds (1607.46 seconds total)