Starting phenix.real_space_refine on Thu Oct 22 20:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zrs_74629/10_2026/9zrs_74629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zrs_74629/10_2026/9zrs_74629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zrs_74629/10_2026/9zrs_74629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zrs_74629/10_2026/9zrs_74629.map" model { file = "/net/cci-nas-00/data/ceres_data/9zrs_74629/10_2026/9zrs_74629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zrs_74629/10_2026/9zrs_74629.cif" } resolution = 3.4 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 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 18 5.16 5 C 3162 2.51 5 N 858 2.21 5 O 997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5035 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1633 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 3 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 862 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 837 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 100} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 892 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Time building chain proxies: 1.15, per 1000 atoms: 0.23 Number of scatterers: 5035 At special positions: 0 Unit cell: (66, 79.2, 124.3, 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 18 16.00 O 997 8.00 N 858 7.00 C 3162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 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: 0.39 Conformation dependent library (CDL) restraints added in 215.3 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 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: 15 helices and 10 sheets defined 28.4% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'D' and resid 43 through 65 removed outlier: 3.687A pdb=" N ASP D 49 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR D 50 " --> pdb=" O MET D 46 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 94 removed outlier: 3.612A pdb=" N GLU D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 148 removed outlier: 3.526A pdb=" N SER D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'D' and resid 159 through 176 removed outlier: 3.860A pdb=" N ALA D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.873A pdb=" N ALA D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 198' Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 250 through 258 removed outlier: 3.654A pdb=" N MET D 256 " --> pdb=" O PRO D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 320 removed outlier: 3.736A pdb=" N ALA D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 294 " --> pdb=" O MET D 290 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLN D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.230A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.714A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.531A pdb=" N LYS O 64 " --> pdb=" O PRO O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.576A pdb=" N THR O 87 " --> pdb=" O THR O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.109A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 235 through 240 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.528A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.706A pdb=" N GLY H 58 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR H 90 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL H 106 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.657A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.717A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG L 46 " --> pdb=" O HIS L 37 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ARG L 39 " --> pdb=" O PRO L 44 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 6 through 7 Processing sheet with id=AA7, first strand: chain 'O' and resid 57 through 59 removed outlier: 5.164A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.675A pdb=" N ILE P 75 " --> pdb=" O VAL P 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 11 through 12 removed outlier: 6.698A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'P' and resid 53 through 54 removed outlier: 6.516A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 591 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: 0.58 Time building geometry restraints manager: 0.55 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: 1549 1.34 - 1.46: 1022 1.46 - 1.58: 2538 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 5137 Sorted by residual: bond pdb=" N ASN D 224 " pdb=" CA ASN D 224 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 6.80e+00 bond pdb=" N LYS L 74 " pdb=" CA LYS L 74 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.18e-02 7.18e+03 6.57e+00 bond pdb=" N ILE D 234 " pdb=" CA ILE D 234 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.30e-02 5.92e+03 6.47e+00 bond pdb=" N ILE L 75 " pdb=" CA ILE L 75 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.94e+00 bond pdb=" N GLN P 3 " pdb=" CA GLN P 3 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.21e-02 6.83e+03 5.94e+00 ... (remaining 5132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 6661 2.50 - 5.00: 255 5.00 - 7.50: 41 7.50 - 10.00: 12 10.00 - 12.50: 3 Bond angle restraints: 6972 Sorted by residual: angle pdb=" CB LYS D 72 " pdb=" CG LYS D 72 " pdb=" CD LYS D 72 " ideal model delta sigma weight residual 111.30 121.77 -10.47 2.30e+00 1.89e-01 2.07e+01 angle pdb=" N ILE D 234 " pdb=" CA ILE D 234 " pdb=" C ILE D 234 " ideal model delta sigma weight residual 113.22 107.71 5.51 1.23e+00 6.61e-01 2.01e+01 angle pdb=" C LEU H 63 " pdb=" N LYS H 64 " pdb=" CA LYS H 64 " ideal model delta sigma weight residual 123.04 129.05 -6.01 1.46e+00 4.69e-01 1.70e+01 angle pdb=" N PRO L 44 " pdb=" CA PRO L 44 " pdb=" CB PRO L 44 " ideal model delta sigma weight residual 103.25 99.66 3.59 8.80e-01 1.29e+00 1.66e+01 angle pdb=" C ALA P 50 " pdb=" N ALA P 51 " pdb=" CA ALA P 51 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 ... (remaining 6967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.94: 2660 13.94 - 27.87: 311 27.87 - 41.81: 73 41.81 - 55.75: 23 55.75 - 69.68: 6 Dihedral angle restraints: 3073 sinusoidal: 1191 harmonic: 1882 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 47.22 45.78 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CA ASN H 76 " pdb=" C ASN H 76 " pdb=" N GLN H 77 " pdb=" CA GLN H 77 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLN D 295 " pdb=" C GLN D 295 " pdb=" N THR D 296 " pdb=" CA THR D 296 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 3070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 669 0.080 - 0.159: 104 0.159 - 0.239: 12 0.239 - 0.318: 2 0.318 - 0.397: 1 Chirality restraints: 788 Sorted by residual: chirality pdb=" CB VAL D 218 " pdb=" CA VAL D 218 " pdb=" CG1 VAL D 218 " pdb=" CG2 VAL D 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB THR H 87 " pdb=" CA THR H 87 " pdb=" OG1 THR H 87 " pdb=" CG2 THR H 87 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL H 29 " pdb=" CA VAL H 29 " pdb=" CG1 VAL H 29 " pdb=" CG2 VAL H 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 785 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 164 " -0.005 2.00e-02 2.50e+03 1.71e-02 5.83e+00 pdb=" CG TYR D 164 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 164 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 164 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR D 164 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 164 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 164 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 164 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 58 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO L 59 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 287 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" CG ASP D 287 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP D 287 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP D 287 " -0.014 2.00e-02 2.50e+03 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1583 2.84 - 3.35: 4155 3.35 - 3.87: 8482 3.87 - 4.38: 9336 4.38 - 4.90: 16528 Nonbonded interactions: 40084 Sorted by model distance: nonbonded pdb=" OD1 ASN O 82A" pdb=" N SER O 82B" model vdw 2.323 3.120 nonbonded pdb=" O GLN O 3 " pdb=" OG SER O 25 " model vdw 2.361 3.040 nonbonded pdb=" NE2 GLN P 6 " pdb=" OG1 THR P 102 " model vdw 2.363 3.120 nonbonded pdb=" O LEU H 20 " pdb=" OG SER H 79 " model vdw 2.367 3.040 nonbonded pdb=" O LYS D 62 " pdb=" OG SER D 66 " model vdw 2.373 3.040 ... (remaining 40079 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: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.090 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.006 0.055 5141 Z= 0.315 Angle : 1.128 12.504 6980 Z= 0.619 Chirality : 0.059 0.397 788 Planarity : 0.007 0.060 889 Dihedral : 13.365 69.681 1855 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -3.56 (0.27), residues: 640 helix: -4.03 (0.18), residues: 158 sheet: -1.34 (0.35), residues: 199 loop : -1.94 (0.30), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG L 77 TYR 0.039 0.003 TYR D 164 PHE 0.016 0.003 PHE D 167 TRP 0.022 0.002 TRP D 226 HIS 0.010 0.002 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.31 ( 5137) covalent geometry : angle 1.12870 / 0.62 ( 6972) SS BOND : bond 0.00507 / 0.26 ( 4) SS BOND : angle 0.90268 / 0.50 ( 8) hydrogen bonds : bond 0.27605 / 18.73 ( 216) hydrogen bonds : angle 10.53754 / 7.07 ( 591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.222 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0796 time to fit residues: 12.8155 Evaluate side-chains 96 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [54, 24, 48, 56, 26, 2, 16, 61, 32, 31, 25] chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.0000 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 58 ASN D 146 ASN D 293 ASN D 310 ASN P 37 GLN P 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.166248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140267 restraints weight = 7220.795| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.84 r_work: 0.3727 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5141 Z= 0.159 Angle : 0.648 10.072 6980 Z= 0.332 Chirality : 0.044 0.174 788 Planarity : 0.005 0.040 889 Dihedral : 4.786 19.860 696 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.06 % Allowed : 10.27 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -2.22 (0.29), residues: 640 helix: -1.57 (0.33), residues: 161 sheet: -1.21 (0.35), residues: 202 loop : -1.43 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 61 TYR 0.017 0.002 TYR D 301 PHE 0.016 0.002 PHE O 78 TRP 0.019 0.002 TRP D 226 HIS 0.008 0.001 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 5137) covalent geometry : angle 0.64843 / 0.33 ( 6972) SS BOND : bond 0.00540 / 0.27 ( 4) SS BOND : angle 0.69436 / 0.38 ( 8) hydrogen bonds : bond 0.04037 / 2.72 ( 216) hydrogen bonds : angle 6.08891 / 4.06 ( 591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: D 229 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7852 (tp30) REVERT: H 3 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7639 (tm-30) REVERT: L 39 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7262 (mtp85) REVERT: O 81 LYS cc_start: 0.6055 (ttpp) cc_final: 0.5648 (mptt) REVERT: O 103 TRP cc_start: 0.7937 (m100) cc_final: 0.7209 (m100) outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 0.0742 time to fit residues: 10.9306 Evaluate side-chains 106 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [30, 0, 33, 52, 38, 46, 25, 45, 51, 54, 21] chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 58 ASN D 241 ASN D 293 ASN D 310 ASN O 95 HIS O 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.175286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.153780 restraints weight = 6923.361| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.95 r_work: 0.3930 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5141 Z= 0.174 Angle : 0.622 9.645 6980 Z= 0.313 Chirality : 0.044 0.191 788 Planarity : 0.004 0.051 889 Dihedral : 4.640 19.045 696 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.42 % Allowed : 13.45 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -1.47 (0.31), residues: 640 helix: -0.14 (0.38), residues: 161 sheet: -1.21 (0.35), residues: 208 loop : -1.12 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 77 TYR 0.019 0.002 TYR D 301 PHE 0.016 0.002 PHE O 78 TRP 0.018 0.001 TRP D 226 HIS 0.004 0.001 HIS O 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 5137) covalent geometry : angle 0.62200 / 0.31 ( 6972) SS BOND : bond 0.00455 / 0.22 ( 4) SS BOND : angle 0.59214 / 0.33 ( 8) hydrogen bonds : bond 0.03580 / 2.41 ( 216) hydrogen bonds : angle 5.59803 / 3.74 ( 591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.121 Fit side-chains REVERT: D 94 GLN cc_start: 0.6878 (pp30) cc_final: 0.6675 (pp30) REVERT: L 39 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7219 (mtp85) REVERT: O 103 TRP cc_start: 0.7791 (m100) cc_final: 0.7169 (m100) outliers start: 8 outliers final: 7 residues processed: 116 average time/residue: 0.0747 time to fit residues: 11.0416 Evaluate side-chains 106 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain P residue 91 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [37, 57, 41, 15, 38, 0, 27, 34, 21, 47, 25] chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 58 ASN D 310 ASN H 39 GLN H 77 GLN L 38 GLN O 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.169810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.147455 restraints weight = 6930.853| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.96 r_work: 0.3854 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5141 Z= 0.240 Angle : 0.684 8.365 6980 Z= 0.347 Chirality : 0.045 0.169 788 Planarity : 0.004 0.040 889 Dihedral : 4.820 21.033 696 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.83 % Allowed : 14.51 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -1.33 (0.31), residues: 640 helix: 0.62 (0.40), residues: 161 sheet: -1.32 (0.34), residues: 203 loop : -1.33 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 94 TYR 0.023 0.002 TYR D 301 PHE 0.020 0.002 PHE O 78 TRP 0.017 0.002 TRP D 226 HIS 0.005 0.001 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 ( 5137) covalent geometry : angle 0.68359 / 0.35 ( 6972) SS BOND : bond 0.00689 / 0.34 ( 4) SS BOND : angle 0.82665 / 0.45 ( 8) hydrogen bonds : bond 0.03554 / 2.36 ( 216) hydrogen bonds : angle 5.66025 / 3.78 ( 591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: D 92 SER cc_start: 0.8501 (m) cc_final: 0.8273 (p) REVERT: P 3 GLN cc_start: 0.8345 (mp10) cc_final: 0.7815 (mp10) REVERT: P 4 MET cc_start: 0.7403 (mmt) cc_final: 0.6396 (mmm) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 0.0804 time to fit residues: 12.3990 Evaluate side-chains 110 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 91 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [11, 34, 7, 42, 32, 41, 29, 36, 20, 28, 16] chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 0.0570 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.0270 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 310 ASN H 77 GLN O 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.175601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.154192 restraints weight = 6909.330| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.93 r_work: 0.3956 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5141 Z= 0.115 Angle : 0.572 9.720 6980 Z= 0.284 Chirality : 0.042 0.183 788 Planarity : 0.004 0.040 889 Dihedral : 4.360 19.714 696 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.77 % Allowed : 17.35 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.95 (0.32), residues: 640 helix: 1.13 (0.41), residues: 159 sheet: -1.05 (0.36), residues: 191 loop : -1.27 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 39 TYR 0.010 0.001 TYR D 301 PHE 0.013 0.001 PHE O 78 TRP 0.016 0.001 TRP D 226 HIS 0.002 0.000 HIS D 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 5137) covalent geometry : angle 0.57165 / 0.28 ( 6972) SS BOND : bond 0.00460 / 0.23 ( 4) SS BOND : angle 0.62392 / 0.33 ( 8) hydrogen bonds : bond 0.02953 / 1.97 ( 216) hydrogen bonds : angle 5.00629 / 3.35 ( 591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.194 Fit side-chains REVERT: D 200 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7931 (mp0) REVERT: D 256 MET cc_start: 0.8435 (mpp) cc_final: 0.8224 (mpp) REVERT: L 39 ARG cc_start: 0.7418 (tpp80) cc_final: 0.7051 (ttm-80) REVERT: O 103 TRP cc_start: 0.7778 (m100) cc_final: 0.6921 (m100) REVERT: P 3 GLN cc_start: 0.8232 (mp10) cc_final: 0.7780 (mp10) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.0724 time to fit residues: 11.5247 Evaluate side-chains 110 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 91 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [35, 49, 52, 7, 15, 3, 33, 44, 38, 56, 5] chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 310 ASN H 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.171779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.149871 restraints weight = 6995.930| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.95 r_work: 0.3886 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5141 Z= 0.187 Angle : 0.643 8.709 6980 Z= 0.322 Chirality : 0.044 0.177 788 Planarity : 0.004 0.041 889 Dihedral : 4.477 21.077 696 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.83 % Allowed : 18.05 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.95 (0.32), residues: 640 helix: 1.32 (0.42), residues: 159 sheet: -1.16 (0.36), residues: 191 loop : -1.32 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 94 TYR 0.016 0.002 TYR L 49 PHE 0.024 0.002 PHE O 78 TRP 0.016 0.002 TRP D 226 HIS 0.003 0.001 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 5137) covalent geometry : angle 0.64278 / 0.32 ( 6972) SS BOND : bond 0.00566 / 0.28 ( 4) SS BOND : angle 0.74687 / 0.41 ( 8) hydrogen bonds : bond 0.03175 / 2.12 ( 216) hydrogen bonds : angle 5.16114 / 3.48 ( 591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.333 Fit side-chains REVERT: D 200 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7609 (mp0) REVERT: O 103 TRP cc_start: 0.7781 (m100) cc_final: 0.7006 (m100) REVERT: P 3 GLN cc_start: 0.8193 (mp10) cc_final: 0.7898 (mp10) outliers start: 16 outliers final: 11 residues processed: 120 average time/residue: 0.0769 time to fit residues: 11.9678 Evaluate side-chains 115 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 91 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [51, 50, 33, 57, 9, 7, 49, 54, 15, 24, 18] chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 310 ASN H 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.172788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151103 restraints weight = 6915.631| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.93 r_work: 0.3881 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5141 Z= 0.161 Angle : 0.643 10.748 6980 Z= 0.317 Chirality : 0.043 0.156 788 Planarity : 0.004 0.040 889 Dihedral : 4.424 21.178 696 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.65 % Allowed : 18.94 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.89 (0.32), residues: 640 helix: 1.38 (0.42), residues: 159 sheet: -1.20 (0.35), residues: 197 loop : -1.20 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 94 TYR 0.014 0.002 TYR D 164 PHE 0.022 0.002 PHE O 78 TRP 0.016 0.002 TRP D 226 HIS 0.004 0.001 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 5137) covalent geometry : angle 0.64290 / 0.32 ( 6972) SS BOND : bond 0.00608 / 0.31 ( 4) SS BOND : angle 0.72983 / 0.40 ( 8) hydrogen bonds : bond 0.03043 / 2.04 ( 216) hydrogen bonds : angle 5.04956 / 3.41 ( 591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.225 Fit side-chains REVERT: D 200 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7676 (mp0) REVERT: H 73 MET cc_start: 0.8282 (mpp) cc_final: 0.7119 (mmm) REVERT: L 39 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.6899 (ttm-80) REVERT: L 77 ARG cc_start: 0.6820 (mtm110) cc_final: 0.6537 (mtm110) REVERT: O 103 TRP cc_start: 0.7814 (m100) cc_final: 0.6963 (m100) REVERT: P 3 GLN cc_start: 0.8342 (mp10) cc_final: 0.7847 (mp10) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.0780 time to fit residues: 11.7385 Evaluate side-chains 115 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 91 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [13, 8, 30, 59, 61, 18, 47, 33, 55, 27, 54] chunk 13 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 59 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 GLN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.174427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.152962 restraints weight = 6979.922| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.93 r_work: 0.3904 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5141 Z= 0.134 Angle : 0.615 9.589 6980 Z= 0.305 Chirality : 0.043 0.151 788 Planarity : 0.004 0.039 889 Dihedral : 4.360 20.756 696 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.12 % Allowed : 19.29 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.82 (0.32), residues: 640 helix: 1.41 (0.42), residues: 159 sheet: -1.14 (0.35), residues: 197 loop : -1.16 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 94 TYR 0.011 0.001 TYR L 49 PHE 0.020 0.001 PHE O 78 TRP 0.015 0.001 TRP D 226 HIS 0.002 0.001 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 5137) covalent geometry : angle 0.61459 / 0.31 ( 6972) SS BOND : bond 0.00471 / 0.23 ( 4) SS BOND : angle 0.69643 / 0.38 ( 8) hydrogen bonds : bond 0.02942 / 1.97 ( 216) hydrogen bonds : angle 4.91181 / 3.33 ( 591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.187 Fit side-chains REVERT: D 200 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7701 (mp0) REVERT: H 73 MET cc_start: 0.8279 (mpp) cc_final: 0.7098 (mmm) REVERT: L 77 ARG cc_start: 0.6775 (mtm110) cc_final: 0.6510 (mtm110) REVERT: O 103 TRP cc_start: 0.7706 (m100) cc_final: 0.6754 (m100) outliers start: 12 outliers final: 11 residues processed: 118 average time/residue: 0.0723 time to fit residues: 11.0032 Evaluate side-chains 119 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 91 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [22, 47, 20, 0, 35, 1, 38, 10, 6, 19, 17] chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.172101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.150800 restraints weight = 6959.549| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.92 r_work: 0.3888 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5141 Z= 0.182 Angle : 0.680 12.536 6980 Z= 0.338 Chirality : 0.044 0.159 788 Planarity : 0.004 0.039 889 Dihedral : 4.517 21.293 696 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.48 % Allowed : 20.88 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.78 (0.33), residues: 640 helix: 1.47 (0.43), residues: 159 sheet: -1.09 (0.36), residues: 197 loop : -1.18 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 94 TYR 0.015 0.002 TYR L 49 PHE 0.021 0.002 PHE O 78 TRP 0.016 0.002 TRP D 226 HIS 0.003 0.001 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 5137) covalent geometry : angle 0.67984 / 0.34 ( 6972) SS BOND : bond 0.00518 / 0.26 ( 4) SS BOND : angle 0.53116 / 0.29 ( 8) hydrogen bonds : bond 0.03121 / 2.08 ( 216) hydrogen bonds : angle 5.06099 / 3.44 ( 591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: D 200 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7608 (mp0) REVERT: H 73 MET cc_start: 0.8248 (mpp) cc_final: 0.7031 (mmm) REVERT: L 77 ARG cc_start: 0.6798 (mtm110) cc_final: 0.6536 (mtm110) REVERT: O 103 TRP cc_start: 0.7814 (m100) cc_final: 0.6910 (m100) outliers start: 14 outliers final: 12 residues processed: 123 average time/residue: 0.0743 time to fit residues: 11.8782 Evaluate side-chains 120 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 91 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [14, 29, 35, 47, 33, 18, 55, 59, 56, 45, 12] chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.171871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.150430 restraints weight = 6909.509| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.93 r_work: 0.3888 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5141 Z= 0.176 Angle : 0.688 11.152 6980 Z= 0.341 Chirality : 0.045 0.155 788 Planarity : 0.004 0.047 889 Dihedral : 4.555 21.565 696 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.12 % Allowed : 21.24 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 (0.32), residues: 640 helix: 1.41 (0.42), residues: 159 sheet: -1.15 (0.36), residues: 191 loop : -1.20 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 94 TYR 0.017 0.002 TYR H 52 PHE 0.020 0.002 PHE O 78 TRP 0.016 0.002 TRP D 226 HIS 0.002 0.001 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 5137) covalent geometry : angle 0.68840 / 0.34 ( 6972) SS BOND : bond 0.00519 / 0.26 ( 4) SS BOND : angle 0.53100 / 0.29 ( 8) hydrogen bonds : bond 0.03166 / 2.08 ( 216) hydrogen bonds : angle 5.08035 / 3.46 ( 591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 200 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7620 (mp0) REVERT: H 73 MET cc_start: 0.8243 (mpp) cc_final: 0.7018 (mmm) REVERT: L 77 ARG cc_start: 0.6849 (mtm110) cc_final: 0.6598 (mtm110) REVERT: O 81 LYS cc_start: 0.6127 (mptt) cc_final: 0.5912 (mptt) REVERT: O 103 TRP cc_start: 0.7807 (m100) cc_final: 0.6880 (m100) REVERT: P 4 MET cc_start: 0.6764 (mmt) cc_final: 0.6549 (mmt) outliers start: 12 outliers final: 11 residues processed: 123 average time/residue: 0.0717 time to fit residues: 11.2973 Evaluate side-chains 121 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 91 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: [36, 23, 31, 8, 3, 4, 37, 9, 52, 13, 21] chunk 36 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.171940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150426 restraints weight = 7025.725| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.95 r_work: 0.3909 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5141 Z= 0.173 Angle : 0.686 11.957 6980 Z= 0.339 Chirality : 0.045 0.178 788 Planarity : 0.004 0.043 889 Dihedral : 4.554 21.355 696 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.48 % Allowed : 21.06 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 (0.32), residues: 640 helix: 1.38 (0.42), residues: 159 sheet: -1.16 (0.36), residues: 191 loop : -1.20 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 94 TYR 0.017 0.002 TYR H 52 PHE 0.019 0.002 PHE O 78 TRP 0.015 0.002 TRP D 226 HIS 0.003 0.001 HIS P 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 5137) covalent geometry : angle 0.68600 / 0.34 ( 6972) SS BOND : bond 0.00505 / 0.25 ( 4) SS BOND : angle 0.52845 / 0.29 ( 8) hydrogen bonds : bond 0.03249 / 2.12 ( 216) hydrogen bonds : angle 5.06109 / 3.46 ( 591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1536.33 seconds wall clock time: 27 minutes 9.30 seconds (1629.30 seconds total)