Starting phenix.real_space_refine on Wed Aug 5 09:51:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jl1_61575/08_2026/9jl1_61575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jl1_61575/08_2026/9jl1_61575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jl1_61575/08_2026/9jl1_61575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jl1_61575/08_2026/9jl1_61575.map" model { file = "/net/cci-nas-00/data/ceres_data/9jl1_61575/08_2026/9jl1_61575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jl1_61575/08_2026/9jl1_61575.cif" } resolution = 3.5 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= 0.007 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 16 5.16 5 C 5601 2.51 5 N 1579 2.21 5 O 1777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9003 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8358 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 26, 'TRANS': 999} Chain breaks: 5 Chain: "B" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 645 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 25} Time building chain proxies: 1.82, per 1000 atoms: 0.20 Number of scatterers: 9003 At special positions: 0 Unit cell: (91.74, 108.24, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 30 15.00 O 1777 8.00 N 1579 7.00 C 5601 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: 0.63 Conformation dependent library (CDL) restraints added in 220.6 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 55.7% alpha, 9.6% beta 8 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 67 through 92 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.765A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.632A pdb=" N LEU A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 315 through 339 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 369 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.040A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.724A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'A' and resid 771 through 792 removed outlier: 3.874A pdb=" N LYS A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 777 " --> pdb=" O GLY A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 829 through 836 removed outlier: 3.575A pdb=" N ARG A 832 " --> pdb=" O ASP A 829 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 833 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N SER A 834 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.506A pdb=" N ASN A 863 " --> pdb=" O SER A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 889 removed outlier: 3.719A pdb=" N VAL A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 925 through 940 Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.289A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.442A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 4.088A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.706A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.379A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1249 through 1262 Processing helix chain 'A' and resid 1263 through 1281 removed outlier: 4.396A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1340 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 5.925A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.341A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA4, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA5, first strand: chain 'A' and resid 1063 through 1066 removed outlier: 6.302A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A1071 " --> pdb=" O ASN A1066 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.580A pdb=" N VAL A1149 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1160 " --> pdb=" O ALA A1147 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A1147 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A1162 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A1145 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 412 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 0.83 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: 2713 1.34 - 1.45: 1367 1.45 - 1.57: 5045 1.57 - 1.69: 59 1.69 - 1.81: 31 Bond restraints: 9215 Sorted by residual: bond pdb=" N ASN A1177 " pdb=" CA ASN A1177 " ideal model delta sigma weight residual 1.463 1.490 -0.027 8.80e-03 1.29e+04 9.32e+00 bond pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.28e-02 6.10e+03 9.28e+00 bond pdb=" N VAL A 801 " pdb=" CA VAL A 801 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.60e+00 bond pdb=" N ASN A 803 " pdb=" CA ASN A 803 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.23e-02 6.61e+03 7.36e+00 bond pdb=" N GLU A 802 " pdb=" CA GLU A 802 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.80e+00 ... (remaining 9210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12047 1.64 - 3.27: 417 3.27 - 4.91: 60 4.91 - 6.55: 6 6.55 - 8.18: 4 Bond angle restraints: 12534 Sorted by residual: angle pdb=" C VAL A 339 " pdb=" N ARG A 340 " pdb=" CA ARG A 340 " ideal model delta sigma weight residual 121.54 129.04 -7.50 1.91e+00 2.74e-01 1.54e+01 angle pdb=" N ASN A 407 " pdb=" CA ASN A 407 " pdb=" C ASN A 407 " ideal model delta sigma weight residual 114.56 109.80 4.76 1.27e+00 6.20e-01 1.40e+01 angle pdb=" O5' U B 90 " pdb=" C5' U B 90 " pdb=" C4' U B 90 " ideal model delta sigma weight residual 109.40 112.08 -2.68 8.00e-01 1.56e+00 1.12e+01 angle pdb=" O5' G B 81 " pdb=" C5' G B 81 " pdb=" C4' G B 81 " ideal model delta sigma weight residual 109.40 111.90 -2.50 8.00e-01 1.56e+00 9.78e+00 angle pdb=" CA ARG A 74 " pdb=" CB ARG A 74 " pdb=" CG ARG A 74 " ideal model delta sigma weight residual 114.10 120.34 -6.24 2.00e+00 2.50e-01 9.74e+00 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 5068 16.68 - 33.36: 448 33.36 - 50.05: 123 50.05 - 66.73: 56 66.73 - 83.41: 14 Dihedral angle restraints: 5709 sinusoidal: 2689 harmonic: 3020 Sorted by residual: dihedral pdb=" CA GLU A 197 " pdb=" C GLU A 197 " pdb=" N GLU A 198 " pdb=" CA GLU A 198 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ARG A 925 " pdb=" C ARG A 925 " pdb=" N GLN A 926 " pdb=" CA GLN A 926 " ideal model delta harmonic sigma weight residual 180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA VAL A 339 " pdb=" C VAL A 339 " pdb=" N ARG A 340 " pdb=" CA ARG A 340 " ideal model delta harmonic sigma weight residual -180.00 -162.37 -17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 5706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 948 0.034 - 0.069: 302 0.069 - 0.103: 114 0.103 - 0.138: 53 0.138 - 0.172: 4 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CG LEU A 184 " pdb=" CB LEU A 184 " pdb=" CD1 LEU A 184 " pdb=" CD2 LEU A 184 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA VAL A 801 " pdb=" N VAL A 801 " pdb=" C VAL A 801 " pdb=" CB VAL A 801 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB ILE A1057 " pdb=" CA ILE A1057 " pdb=" CG1 ILE A1057 " pdb=" CG2 ILE A1057 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1418 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1060 " 0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO A1061 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A1061 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1061 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 315 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 316 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 180 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C ASP A 180 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP A 180 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 181 " -0.012 2.00e-02 2.50e+03 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1578 2.77 - 3.30: 9058 3.30 - 3.84: 15225 3.84 - 4.37: 17409 4.37 - 4.90: 28993 Nonbonded interactions: 72263 Sorted by model distance: nonbonded pdb=" O PHE A1045 " pdb=" NZ LYS A1076 " model vdw 2.239 3.120 nonbonded pdb=" N2 G B 87 " pdb=" O2 C B 91 " model vdw 2.264 2.496 nonbonded pdb=" ND2 ASN A 240 " pdb=" OD1 ASN A 255 " model vdw 2.268 3.120 nonbonded pdb=" O GLN A 817 " pdb=" OH TYR A 882 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLN A1272 " pdb=" N1 G B 89 " model vdw 2.280 3.120 ... (remaining 72258 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9215 Z= 0.196 Angle : 0.695 8.184 12534 Z= 0.427 Chirality : 0.044 0.172 1421 Planarity : 0.005 0.087 1491 Dihedral : 15.098 83.411 3753 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 0.76 % Allowed : 0.87 % Favored : 98.37 % 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: -0.03 (0.26), residues: 1014 helix: 0.69 (0.23), residues: 509 sheet: -0.25 (0.53), residues: 107 loop : -0.77 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.022 0.001 TYR A 72 PHE 0.017 0.001 PHE A 970 TRP 0.010 0.001 TRP A 883 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.20 ( 9215) covalent geometry : angle 0.69537 / 0.43 (12534) hydrogen bonds : bond 0.13513 / 8.89 ( 432) hydrogen bonds : angle 5.87315 / 4.23 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8243 (tp) cc_final: 0.8036 (tt) REVERT: A 195 LEU cc_start: 0.9010 (tp) cc_final: 0.8653 (tt) REVERT: A 1169 MET cc_start: 0.7838 (mpp) cc_final: 0.7599 (mmm) outliers start: 7 outliers final: 1 residues processed: 213 average time/residue: 0.1077 time to fit residues: 29.5844 Evaluate side-chains 106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 912 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 HIS A 726 ASN ** A 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.116244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091879 restraints weight = 30210.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.094313 restraints weight = 16569.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.095869 restraints weight = 11421.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.096818 restraints weight = 9096.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.097319 restraints weight = 7948.699| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9215 Z= 0.161 Angle : 0.684 11.189 12534 Z= 0.358 Chirality : 0.044 0.285 1421 Planarity : 0.005 0.071 1491 Dihedral : 12.780 73.219 1582 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 1.85 % Allowed : 9.80 % Favored : 88.34 % 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: -0.16 (0.25), residues: 1014 helix: 0.54 (0.22), residues: 512 sheet: -0.06 (0.54), residues: 99 loop : -0.86 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 783 TYR 0.021 0.002 TYR A 72 PHE 0.030 0.002 PHE A1008 TRP 0.024 0.003 TRP A 883 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9215) covalent geometry : angle 0.68436 / 0.36 (12534) hydrogen bonds : bond 0.05492 / 3.39 ( 432) hydrogen bonds : angle 4.97788 / 3.52 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASN cc_start: 0.8385 (p0) cc_final: 0.8149 (p0) REVERT: A 74 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8372 (ppt-90) REVERT: A 80 CYS cc_start: 0.9366 (m) cc_final: 0.9046 (p) REVERT: A 195 LEU cc_start: 0.9110 (tp) cc_final: 0.8802 (tt) REVERT: A 256 PHE cc_start: 0.7018 (m-10) cc_final: 0.6697 (m-10) REVERT: A 1057 ILE cc_start: 0.8282 (mm) cc_final: 0.8019 (tp) REVERT: A 1160 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7034 (m) REVERT: A 1169 MET cc_start: 0.8355 (mpp) cc_final: 0.7930 (mmm) REVERT: A 1266 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7771 (tp) outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 0.0857 time to fit residues: 14.3262 Evaluate side-chains 106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.0020 chunk 75 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 GLN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.116800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.092581 restraints weight = 29855.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.095009 restraints weight = 16421.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.096548 restraints weight = 11310.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.097487 restraints weight = 8993.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.098127 restraints weight = 7836.066| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9215 Z= 0.126 Angle : 0.613 9.228 12534 Z= 0.321 Chirality : 0.041 0.208 1421 Planarity : 0.005 0.062 1491 Dihedral : 12.745 73.510 1582 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 1.85 % Allowed : 10.68 % Favored : 87.47 % 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: -0.05 (0.26), residues: 1014 helix: 0.63 (0.23), residues: 507 sheet: 0.08 (0.57), residues: 87 loop : -0.78 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 895 TYR 0.022 0.001 TYR A 72 PHE 0.025 0.001 PHE A1174 TRP 0.028 0.003 TRP A 883 HIS 0.004 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9215) covalent geometry : angle 0.61321 / 0.32 (12534) hydrogen bonds : bond 0.04995 / 3.13 ( 432) hydrogen bonds : angle 4.82982 / 3.40 ( 1218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.9348 (m) cc_final: 0.9048 (p) REVERT: A 195 LEU cc_start: 0.9120 (tp) cc_final: 0.8875 (tt) REVERT: A 377 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7840 (mtmm) REVERT: A 1057 ILE cc_start: 0.8295 (mm) cc_final: 0.8069 (tp) REVERT: A 1169 MET cc_start: 0.8365 (mpp) cc_final: 0.7932 (mmm) REVERT: A 1266 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7791 (tp) outliers start: 17 outliers final: 11 residues processed: 111 average time/residue: 0.0926 time to fit residues: 14.4458 Evaluate side-chains 94 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 726 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN ** A1177 ASN ** 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 = 0.4122 r_free = 0.4122 target = 0.113919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.089396 restraints weight = 30332.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091725 restraints weight = 16711.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.093215 restraints weight = 11598.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.094136 restraints weight = 9312.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.094711 restraints weight = 8130.052| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9215 Z= 0.171 Angle : 0.607 7.653 12534 Z= 0.323 Chirality : 0.041 0.217 1421 Planarity : 0.005 0.069 1491 Dihedral : 12.785 73.599 1582 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 2.18 % Allowed : 12.20 % Favored : 85.62 % 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: 0.01 (0.26), residues: 1014 helix: 0.73 (0.23), residues: 508 sheet: -0.37 (0.54), residues: 88 loop : -0.72 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1060 TYR 0.025 0.002 TYR A1036 PHE 0.016 0.002 PHE A1008 TRP 0.036 0.004 TRP A 883 HIS 0.005 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9215) covalent geometry : angle 0.60679 / 0.32 (12534) hydrogen bonds : bond 0.05081 / 3.17 ( 432) hydrogen bonds : angle 4.80091 / 3.38 ( 1218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.9386 (m) cc_final: 0.9063 (p) REVERT: A 1062 LEU cc_start: 0.7908 (tp) cc_final: 0.7690 (mt) REVERT: A 1169 MET cc_start: 0.8418 (mpp) cc_final: 0.7974 (mmm) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 0.0794 time to fit residues: 11.9072 Evaluate side-chains 90 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 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 = 0.4142 r_free = 0.4142 target = 0.114128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.089749 restraints weight = 30203.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.092035 restraints weight = 16659.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.093459 restraints weight = 11644.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.094341 restraints weight = 9389.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.094797 restraints weight = 8275.232| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9215 Z= 0.187 Angle : 0.605 7.565 12534 Z= 0.322 Chirality : 0.041 0.273 1421 Planarity : 0.004 0.068 1491 Dihedral : 12.823 73.632 1582 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 1.85 % Allowed : 13.83 % Favored : 84.31 % 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: -0.03 (0.26), residues: 1014 helix: 0.70 (0.23), residues: 513 sheet: -0.72 (0.50), residues: 98 loop : -0.65 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.021 0.002 TYR A 814 PHE 0.024 0.002 PHE A1008 TRP 0.041 0.004 TRP A 883 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 9215) covalent geometry : angle 0.60528 / 0.32 (12534) hydrogen bonds : bond 0.05077 / 3.17 ( 432) hydrogen bonds : angle 4.88533 / 3.44 ( 1218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7153 (ttp80) REVERT: A 80 CYS cc_start: 0.9377 (m) cc_final: 0.9059 (p) REVERT: A 328 HIS cc_start: 0.3922 (OUTLIER) cc_final: 0.3143 (t-170) REVERT: A 1062 LEU cc_start: 0.7940 (tp) cc_final: 0.7727 (mt) REVERT: A 1169 MET cc_start: 0.8287 (mpp) cc_final: 0.7897 (mmm) outliers start: 17 outliers final: 15 residues processed: 100 average time/residue: 0.0855 time to fit residues: 12.3800 Evaluate side-chains 94 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS A 721 HIS ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.109732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.085103 restraints weight = 30421.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.087286 restraints weight = 16939.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.088642 restraints weight = 11912.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.089471 restraints weight = 9688.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089942 restraints weight = 8570.560| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9215 Z= 0.320 Angle : 0.759 14.800 12534 Z= 0.401 Chirality : 0.047 0.216 1421 Planarity : 0.006 0.073 1491 Dihedral : 13.082 73.576 1582 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 2.94 % Allowed : 13.94 % Favored : 83.12 % 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: -0.59 (0.25), residues: 1014 helix: 0.39 (0.23), residues: 524 sheet: -1.64 (0.43), residues: 116 loop : -0.95 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1060 TYR 0.023 0.002 TYR A 815 PHE 0.020 0.003 PHE A1313 TRP 0.026 0.004 TRP A 883 HIS 0.007 0.002 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.32 ( 9215) covalent geometry : angle 0.75930 / 0.40 (12534) hydrogen bonds : bond 0.06043 / 3.83 ( 432) hydrogen bonds : angle 5.24551 / 3.69 ( 1218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7745 (ttp80) REVERT: A 80 CYS cc_start: 0.9422 (m) cc_final: 0.9086 (p) REVERT: A 328 HIS cc_start: 0.3964 (OUTLIER) cc_final: 0.3201 (t-90) REVERT: A 1062 LEU cc_start: 0.8203 (tp) cc_final: 0.7988 (mt) REVERT: A 1160 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7884 (m) REVERT: A 1169 MET cc_start: 0.8395 (mpp) cc_final: 0.7998 (mmm) REVERT: A 1197 LYS cc_start: 0.8419 (tttp) cc_final: 0.8219 (tttp) outliers start: 27 outliers final: 17 residues processed: 104 average time/residue: 0.0938 time to fit residues: 13.5486 Evaluate side-chains 90 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 91 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.112283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087083 restraints weight = 30587.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089424 restraints weight = 17094.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.090891 restraints weight = 12001.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.091790 restraints weight = 9734.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.092291 restraints weight = 8593.027| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9215 Z= 0.145 Angle : 0.625 14.664 12534 Z= 0.330 Chirality : 0.042 0.305 1421 Planarity : 0.005 0.087 1491 Dihedral : 12.953 73.801 1580 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.40 % Allowed : 15.58 % Favored : 82.03 % 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: -0.26 (0.26), residues: 1014 helix: 0.66 (0.23), residues: 514 sheet: -1.38 (0.45), residues: 107 loop : -0.82 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1303 TYR 0.019 0.001 TYR A 815 PHE 0.028 0.001 PHE A1008 TRP 0.017 0.002 TRP A 883 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9215) covalent geometry : angle 0.62514 / 0.33 (12534) hydrogen bonds : bond 0.05025 / 3.15 ( 432) hydrogen bonds : angle 5.01636 / 3.55 ( 1218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.9452 (m) cc_final: 0.9106 (p) REVERT: A 328 HIS cc_start: 0.3924 (OUTLIER) cc_final: 0.3221 (t-90) REVERT: A 403 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7985 (tpm170) REVERT: A 822 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6483 (ttm) REVERT: A 1062 LEU cc_start: 0.8066 (tp) cc_final: 0.7800 (mt) REVERT: A 1169 MET cc_start: 0.8371 (mpp) cc_final: 0.7986 (mmm) outliers start: 22 outliers final: 13 residues processed: 99 average time/residue: 0.0912 time to fit residues: 12.9580 Evaluate side-chains 93 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 52 optimal weight: 0.0770 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.111258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.086685 restraints weight = 29828.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.088944 restraints weight = 16528.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.090345 restraints weight = 11574.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.091223 restraints weight = 9356.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.091738 restraints weight = 8241.934| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9215 Z= 0.174 Angle : 0.618 13.718 12534 Z= 0.327 Chirality : 0.042 0.194 1421 Planarity : 0.005 0.066 1491 Dihedral : 12.932 73.689 1580 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.96 % Allowed : 16.45 % Favored : 81.59 % 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: -0.28 (0.26), residues: 1014 helix: 0.67 (0.23), residues: 515 sheet: -1.56 (0.43), residues: 114 loop : -0.79 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1303 TYR 0.021 0.002 TYR A 814 PHE 0.020 0.001 PHE A1008 TRP 0.013 0.002 TRP A 883 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9215) covalent geometry : angle 0.61802 / 0.33 (12534) hydrogen bonds : bond 0.04996 / 3.14 ( 432) hydrogen bonds : angle 5.02612 / 3.56 ( 1218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.9420 (m) cc_final: 0.9091 (p) REVERT: A 132 TYR cc_start: 0.8192 (m-10) cc_final: 0.7988 (m-10) REVERT: A 328 HIS cc_start: 0.3955 (OUTLIER) cc_final: 0.3219 (t-90) REVERT: A 822 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6492 (ttm) REVERT: A 1169 MET cc_start: 0.8321 (mpp) cc_final: 0.7928 (mmm) outliers start: 18 outliers final: 16 residues processed: 93 average time/residue: 0.0917 time to fit residues: 11.9702 Evaluate side-chains 92 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.112267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.087781 restraints weight = 29901.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.090070 restraints weight = 16562.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.091522 restraints weight = 11549.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.092291 restraints weight = 9303.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.092938 restraints weight = 8254.738| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9215 Z= 0.138 Angle : 0.631 15.241 12534 Z= 0.330 Chirality : 0.042 0.292 1421 Planarity : 0.005 0.086 1491 Dihedral : 12.902 73.724 1580 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.74 % Allowed : 16.88 % Favored : 81.37 % 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: -0.17 (0.26), residues: 1014 helix: 0.73 (0.23), residues: 513 sheet: -1.30 (0.45), residues: 108 loop : -0.75 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 78 TYR 0.014 0.001 TYR A 814 PHE 0.025 0.001 PHE A1008 TRP 0.013 0.002 TRP A 883 HIS 0.004 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9215) covalent geometry : angle 0.63108 / 0.33 (12534) hydrogen bonds : bond 0.04735 / 2.98 ( 432) hydrogen bonds : angle 4.96876 / 3.52 ( 1218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.9432 (m) cc_final: 0.9107 (p) REVERT: A 132 TYR cc_start: 0.8215 (m-10) cc_final: 0.8014 (m-10) REVERT: A 328 HIS cc_start: 0.3844 (OUTLIER) cc_final: 0.3167 (t-90) REVERT: A 1169 MET cc_start: 0.8340 (mpp) cc_final: 0.7972 (mmm) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.0698 time to fit residues: 9.3809 Evaluate side-chains 85 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 990 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 = 0.4072 r_free = 0.4072 target = 0.109706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.085209 restraints weight = 30841.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.087428 restraints weight = 17464.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087783 restraints weight = 11418.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.088073 restraints weight = 11949.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088284 restraints weight = 10443.145| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9215 Z= 0.228 Angle : 0.683 14.186 12534 Z= 0.362 Chirality : 0.044 0.243 1421 Planarity : 0.005 0.073 1491 Dihedral : 13.018 73.560 1580 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.85 % Allowed : 17.10 % Favored : 81.05 % 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: -0.46 (0.26), residues: 1014 helix: 0.50 (0.23), residues: 528 sheet: -1.46 (0.44), residues: 112 loop : -0.95 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.018 0.002 TYR A 815 PHE 0.017 0.002 PHE A1313 TRP 0.014 0.003 TRP A 883 HIS 0.008 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 ( 9215) covalent geometry : angle 0.68268 / 0.36 (12534) hydrogen bonds : bond 0.05445 / 3.44 ( 432) hydrogen bonds : angle 5.10651 / 3.60 ( 1218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.9485 (m) cc_final: 0.9166 (p) REVERT: A 328 HIS cc_start: 0.3935 (OUTLIER) cc_final: 0.3209 (t-90) REVERT: A 1169 MET cc_start: 0.8468 (mpp) cc_final: 0.8212 (mmm) outliers start: 17 outliers final: 15 residues processed: 85 average time/residue: 0.0671 time to fit residues: 8.3959 Evaluate side-chains 83 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 89 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 844 GLN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN ** A1317 ASN ** 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 = 0.4108 r_free = 0.4108 target = 0.111681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087433 restraints weight = 29557.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089703 restraints weight = 16246.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.091158 restraints weight = 11316.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.091907 restraints weight = 9098.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.092510 restraints weight = 8085.668| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9215 Z= 0.133 Angle : 0.633 15.662 12534 Z= 0.330 Chirality : 0.042 0.263 1421 Planarity : 0.004 0.062 1491 Dihedral : 12.948 73.634 1580 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.63 % Allowed : 17.76 % Favored : 80.61 % 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: -0.24 (0.26), residues: 1014 helix: 0.65 (0.23), residues: 516 sheet: -1.25 (0.45), residues: 108 loop : -0.80 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.016 0.001 TYR A 815 PHE 0.026 0.001 PHE A1008 TRP 0.014 0.002 TRP A 883 HIS 0.004 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9215) covalent geometry : angle 0.63295 / 0.33 (12534) hydrogen bonds : bond 0.04695 / 2.95 ( 432) hydrogen bonds : angle 4.98963 / 3.52 ( 1218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.46 seconds wall clock time: 28 minutes 11.17 seconds (1691.17 seconds total)