Starting phenix.real_space_refine on Wed Sep 17 05:20:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7t_47689/09_2025/9e7t_47689.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7t_47689/09_2025/9e7t_47689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e7t_47689/09_2025/9e7t_47689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7t_47689/09_2025/9e7t_47689.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7t_47689/09_2025/9e7t_47689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7t_47689/09_2025/9e7t_47689.cif" } resolution = 2.8 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= 0.037 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 Mg 1 5.21 5 S 28 5.16 5 C 3104 2.51 5 N 795 2.21 5 O 914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1835 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 9, 'TRANS': 215} Chain: "C" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2077 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.32 Number of scatterers: 4842 At special positions: 0 Unit cell: (65.88, 81.252, 109.068, 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 28 16.00 Mg 1 11.99 O 914 8.00 N 795 7.00 C 3104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 186.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 55.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 48 through 51 removed outlier: 4.376A pdb=" N ARG A 51 " --> pdb=" O GLY A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'B' and resid 1094 through 1105 removed outlier: 3.663A pdb=" N ASN B1105 " --> pdb=" O PHE B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1122 Processing helix chain 'B' and resid 1126 through 1138 Processing helix chain 'B' and resid 1145 through 1157 removed outlier: 3.822A pdb=" N TYR B1149 " --> pdb=" O PHE B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1178 Processing helix chain 'B' and resid 1185 through 1204 Processing helix chain 'B' and resid 1216 through 1228 Processing helix chain 'B' and resid 1229 through 1243 removed outlier: 3.654A pdb=" N LEU B1233 " --> pdb=" O GLN B1229 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B1234 " --> pdb=" O GLN B1230 " (cutoff:3.500A) Proline residue: B1237 - end of helix Processing helix chain 'B' and resid 1244 through 1249 removed outlier: 3.765A pdb=" N ILE B1247 " --> pdb=" O GLU B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1256 through 1271 removed outlier: 3.520A pdb=" N VAL B1265 " --> pdb=" O ALA B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1276 through 1290 removed outlier: 3.533A pdb=" N GLU B1282 " --> pdb=" O ASN B1278 " (cutoff:3.500A) Processing helix chain 'B' and resid 1301 through 1305 removed outlier: 3.608A pdb=" N ASP B1305 " --> pdb=" O LEU B1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 34 removed outlier: 3.506A pdb=" N LYS C 25 " --> pdb=" O ASP C 21 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 33 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 70 removed outlier: 3.794A pdb=" N TYR C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 120 removed outlier: 3.695A pdb=" N SER C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 Processing helix chain 'C' and resid 132 through 142 removed outlier: 4.015A pdb=" N THR C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.787A pdb=" N LEU C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 226 through 245 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.578A pdb=" N CYS C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 46 removed outlier: 6.829A pdb=" N VAL A 14 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A 33 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 12 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 101 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 15 removed outlier: 6.435A pdb=" N TRP C 153 " --> pdb=" O TYR C 193 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 702 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: 0.71 Time building geometry restraints manager: 0.57 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: 1562 1.34 - 1.46: 1006 1.46 - 1.58: 2318 1.58 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 4933 Sorted by residual: bond pdb=" CA GLY C 91 " pdb=" C GLY C 91 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.45e+00 bond pdb=" N GLY C 91 " pdb=" CA GLY C 91 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.80e+00 bond pdb=" C PRO B1254 " pdb=" N PRO B1255 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.04e+00 bond pdb=" CB LYS C 33 " pdb=" CG LYS C 33 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.33e-01 bond pdb=" CB MET B1260 " pdb=" CG MET B1260 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 4.12e-01 ... (remaining 4928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 6458 1.09 - 2.18: 152 2.18 - 3.28: 38 3.28 - 4.37: 2 4.37 - 5.46: 4 Bond angle restraints: 6654 Sorted by residual: angle pdb=" N PRO B1254 " pdb=" CA PRO B1254 " pdb=" C PRO B1254 " ideal model delta sigma weight residual 110.70 113.95 -3.25 1.22e+00 6.72e-01 7.10e+00 angle pdb=" CA PRO B1254 " pdb=" C PRO B1254 " pdb=" N PRO B1255 " ideal model delta sigma weight residual 117.93 120.94 -3.01 1.20e+00 6.94e-01 6.28e+00 angle pdb=" N GLU C 214 " pdb=" CA GLU C 214 " pdb=" C GLU C 214 " ideal model delta sigma weight residual 114.75 112.24 2.51 1.26e+00 6.30e-01 3.97e+00 angle pdb=" N SER A 38 " pdb=" CA SER A 38 " pdb=" C SER A 38 " ideal model delta sigma weight residual 110.97 113.10 -2.13 1.09e+00 8.42e-01 3.80e+00 angle pdb=" CB MET B1260 " pdb=" CG MET B1260 " pdb=" SD MET B1260 " ideal model delta sigma weight residual 112.70 107.24 5.46 3.00e+00 1.11e-01 3.31e+00 ... (remaining 6649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 2502 17.71 - 35.42: 330 35.42 - 53.13: 128 53.13 - 70.83: 27 70.83 - 88.54: 7 Dihedral angle restraints: 2994 sinusoidal: 1243 harmonic: 1751 Sorted by residual: dihedral pdb=" CA ALA C 213 " pdb=" C ALA C 213 " pdb=" N GLU C 214 " pdb=" CA GLU C 214 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP A 108 " pdb=" CB ASP A 108 " pdb=" CG ASP A 108 " pdb=" OD1 ASP A 108 " ideal model delta sinusoidal sigma weight residual -30.00 -88.80 58.80 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP C 111 " pdb=" CB ASP C 111 " pdb=" CG ASP C 111 " pdb=" OD1 ASP C 111 " ideal model delta sinusoidal sigma weight residual -30.00 -87.75 57.75 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 2991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 398 0.025 - 0.050: 233 0.050 - 0.075: 71 0.075 - 0.100: 22 0.100 - 0.124: 19 Chirality restraints: 743 Sorted by residual: chirality pdb=" CA ILE C 221 " pdb=" N ILE C 221 " pdb=" C ILE C 221 " pdb=" CB ILE C 221 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 6 " pdb=" N ILE A 6 " pdb=" C ILE A 6 " pdb=" CB ILE A 6 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE B1210 " pdb=" N ILE B1210 " pdb=" C ILE B1210 " pdb=" CB ILE B1210 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 740 not shown) Planarity restraints: 850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1254 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B1255 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B1255 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B1255 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B1253 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO B1254 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B1254 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B1254 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B1236 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO B1237 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B1237 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B1237 " 0.015 5.00e-02 4.00e+02 ... (remaining 847 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 28 2.55 - 3.14: 3434 3.14 - 3.73: 7250 3.73 - 4.31: 11144 4.31 - 4.90: 18385 Nonbonded interactions: 40241 Sorted by model distance: nonbonded pdb=" OE2 GLU C 42 " pdb="MG MG C 301 " model vdw 1.967 2.170 nonbonded pdb=" OH TYR C 193 " pdb=" OD1 ASP C 252 " model vdw 2.196 3.040 nonbonded pdb=" O PRO C 223 " pdb=" OG SER C 229 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR C 62 " pdb=" O PRO C 175 " model vdw 2.243 3.040 nonbonded pdb=" OD2 ASP A 108 " pdb=" OG SER A 110 " model vdw 2.273 3.040 ... (remaining 40236 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:8.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 0.031 4933 Z= 0.122 Angle : 0.455 5.460 6654 Z= 0.249 Chirality : 0.037 0.124 743 Planarity : 0.003 0.035 850 Dihedral : 18.854 88.542 1858 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.29 % Allowed : 26.62 % Favored : 72.09 % 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 aren not related in a simple way. whole: -1.37 (0.32), residues: 589 helix: -1.14 (0.27), residues: 306 sheet: -0.06 (0.64), residues: 61 loop : -0.50 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1171 TYR 0.011 0.001 TYR C 34 PHE 0.008 0.001 PHE B1238 TRP 0.009 0.001 TRP B1198 HIS 0.003 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4933) covalent geometry : angle 0.45540 ( 6654) hydrogen bonds : bond 0.25829 ( 240) hydrogen bonds : angle 7.97793 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.202 Fit side-chains REVERT: B 1180 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: C 40 ASP cc_start: 0.8567 (t0) cc_final: 0.8367 (t0) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.7072 time to fit residues: 51.9254 Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 1098 LYS Chi-restraints excluded: chain B residue 1180 ASP Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134606 restraints weight = 5081.282| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.35 r_work: 0.3376 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4933 Z= 0.154 Angle : 0.523 4.690 6654 Z= 0.284 Chirality : 0.040 0.133 743 Planarity : 0.004 0.040 850 Dihedral : 6.295 52.585 649 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.77 % Allowed : 23.29 % Favored : 73.94 % 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 aren not related in a simple way. whole: -0.08 (0.34), residues: 589 helix: 0.37 (0.30), residues: 302 sheet: -0.12 (0.62), residues: 61 loop : -0.44 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1171 TYR 0.017 0.002 TYR C 62 PHE 0.012 0.001 PHE C 239 TRP 0.009 0.001 TRP B1198 HIS 0.003 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4933) covalent geometry : angle 0.52325 ( 6654) hydrogen bonds : bond 0.05009 ( 240) hydrogen bonds : angle 4.87946 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.198 Fit side-chains REVERT: A 33 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 102 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8085 (mtp) REVERT: A 122 ILE cc_start: 0.8084 (pt) cc_final: 0.7844 (pt) REVERT: B 1124 GLU cc_start: 0.6974 (tp30) cc_final: 0.6694 (tp30) REVERT: B 1225 TYR cc_start: 0.8216 (t80) cc_final: 0.7910 (t80) REVERT: C 55 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5386 (ptp-110) REVERT: C 105 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7047 (mm-30) outliers start: 15 outliers final: 4 residues processed: 76 average time/residue: 0.7383 time to fit residues: 57.9834 Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 1296 GLU Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1229 GLN B1301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133874 restraints weight = 5067.902| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.38 r_work: 0.3395 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4933 Z= 0.165 Angle : 0.521 4.789 6654 Z= 0.280 Chirality : 0.040 0.133 743 Planarity : 0.004 0.043 850 Dihedral : 5.486 49.711 641 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.59 % Allowed : 23.84 % Favored : 73.57 % 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 aren not related in a simple way. whole: 0.10 (0.34), residues: 589 helix: 0.53 (0.29), residues: 312 sheet: -0.04 (0.62), residues: 61 loop : -0.41 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1308 TYR 0.018 0.002 TYR C 62 PHE 0.014 0.002 PHE C 239 TRP 0.008 0.001 TRP B1198 HIS 0.004 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 4933) covalent geometry : angle 0.52079 ( 6654) hydrogen bonds : bond 0.04519 ( 240) hydrogen bonds : angle 4.59243 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.216 Fit side-chains REVERT: A 33 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8516 (t) REVERT: A 102 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8116 (mtp) REVERT: B 1124 GLU cc_start: 0.7020 (tp30) cc_final: 0.6717 (tp30) REVERT: B 1225 TYR cc_start: 0.8239 (t80) cc_final: 0.7910 (t80) REVERT: B 1304 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7460 (mtmt) REVERT: C 55 ARG cc_start: 0.6037 (OUTLIER) cc_final: 0.5435 (ptp-110) outliers start: 14 outliers final: 5 residues processed: 69 average time/residue: 0.7418 time to fit residues: 52.9710 Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 1127 MET Chi-restraints excluded: chain B residue 1296 GLU Chi-restraints excluded: chain B residue 1304 LYS Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1229 GLN B1301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.154576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133866 restraints weight = 5057.230| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.34 r_work: 0.3369 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4933 Z= 0.194 Angle : 0.551 5.143 6654 Z= 0.293 Chirality : 0.041 0.135 743 Planarity : 0.004 0.047 850 Dihedral : 5.440 50.424 641 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.22 % Allowed : 23.48 % Favored : 74.31 % 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 aren not related in a simple way. whole: 0.12 (0.34), residues: 589 helix: 0.59 (0.29), residues: 312 sheet: -0.02 (0.62), residues: 61 loop : -0.48 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1308 TYR 0.019 0.002 TYR C 62 PHE 0.015 0.002 PHE C 239 TRP 0.009 0.002 TRP B1198 HIS 0.005 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 4933) covalent geometry : angle 0.55079 ( 6654) hydrogen bonds : bond 0.04542 ( 240) hydrogen bonds : angle 4.50340 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.212 Fit side-chains REVERT: A 102 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: B 1124 GLU cc_start: 0.7122 (tp30) cc_final: 0.6822 (tp30) REVERT: B 1225 TYR cc_start: 0.8291 (t80) cc_final: 0.7919 (t80) REVERT: B 1304 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7461 (mtmt) REVERT: C 55 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5458 (ptp-110) outliers start: 12 outliers final: 4 residues processed: 68 average time/residue: 0.7176 time to fit residues: 50.5442 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 1296 GLU Chi-restraints excluded: chain B residue 1304 LYS Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B1301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135624 restraints weight = 5102.945| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.40 r_work: 0.3417 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4933 Z= 0.117 Angle : 0.460 4.663 6654 Z= 0.250 Chirality : 0.038 0.127 743 Planarity : 0.003 0.046 850 Dihedral : 4.387 22.353 636 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.59 % Allowed : 23.11 % Favored : 74.31 % 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 aren not related in a simple way. whole: 0.54 (0.35), residues: 589 helix: 1.05 (0.30), residues: 309 sheet: 0.05 (0.63), residues: 61 loop : -0.44 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1308 TYR 0.016 0.001 TYR C 62 PHE 0.011 0.001 PHE C 239 TRP 0.008 0.001 TRP B1198 HIS 0.002 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4933) covalent geometry : angle 0.46037 ( 6654) hydrogen bonds : bond 0.03653 ( 240) hydrogen bonds : angle 4.32231 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.259 Fit side-chains REVERT: A 11 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7980 (ttmt) REVERT: A 33 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8485 (t) REVERT: A 102 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: B 1124 GLU cc_start: 0.7071 (tp30) cc_final: 0.6758 (tp30) REVERT: B 1225 TYR cc_start: 0.8199 (t80) cc_final: 0.7835 (t80) REVERT: B 1304 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7434 (mtmt) REVERT: C 55 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5420 (ptp-110) REVERT: C 105 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7120 (mt-10) outliers start: 14 outliers final: 3 residues processed: 71 average time/residue: 0.6918 time to fit residues: 50.8802 Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 1296 GLU Chi-restraints excluded: chain B residue 1304 LYS Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133681 restraints weight = 5157.182| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.43 r_work: 0.3396 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4933 Z= 0.155 Angle : 0.508 4.836 6654 Z= 0.271 Chirality : 0.039 0.131 743 Planarity : 0.004 0.047 850 Dihedral : 4.490 22.380 636 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.77 % Allowed : 23.11 % Favored : 74.12 % 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 aren not related in a simple way. whole: 0.48 (0.35), residues: 589 helix: 0.93 (0.30), residues: 313 sheet: 0.08 (0.63), residues: 61 loop : -0.40 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1308 TYR 0.018 0.002 TYR C 62 PHE 0.014 0.002 PHE C 239 TRP 0.010 0.001 TRP B1198 HIS 0.004 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4933) covalent geometry : angle 0.50801 ( 6654) hydrogen bonds : bond 0.04036 ( 240) hydrogen bonds : angle 4.34205 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.236 Fit side-chains REVERT: A 11 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7978 (ttmt) REVERT: A 33 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8499 (t) REVERT: A 102 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8131 (mtp) REVERT: B 1124 GLU cc_start: 0.7086 (tp30) cc_final: 0.6768 (tp30) REVERT: B 1225 TYR cc_start: 0.8218 (t80) cc_final: 0.7811 (t80) REVERT: B 1304 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7405 (mtmt) REVERT: C 55 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.5784 (ptp90) REVERT: C 105 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7109 (mt-10) outliers start: 15 outliers final: 5 residues processed: 68 average time/residue: 0.7392 time to fit residues: 51.9995 Evaluate side-chains 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 1127 MET Chi-restraints excluded: chain B residue 1296 GLU Chi-restraints excluded: chain B residue 1304 LYS Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133907 restraints weight = 5053.731| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.46 r_work: 0.3371 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4933 Z= 0.144 Angle : 0.498 4.717 6654 Z= 0.266 Chirality : 0.039 0.129 743 Planarity : 0.004 0.045 850 Dihedral : 4.446 22.322 636 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.85 % Allowed : 23.84 % Favored : 74.31 % 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 aren not related in a simple way. whole: 0.56 (0.35), residues: 589 helix: 1.06 (0.30), residues: 309 sheet: 0.09 (0.63), residues: 61 loop : -0.42 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1308 TYR 0.018 0.001 TYR C 62 PHE 0.014 0.001 PHE C 239 TRP 0.009 0.001 TRP B1198 HIS 0.003 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4933) covalent geometry : angle 0.49848 ( 6654) hydrogen bonds : bond 0.03912 ( 240) hydrogen bonds : angle 4.29982 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.201 Fit side-chains REVERT: A 11 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7951 (ttmt) REVERT: A 33 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8488 (t) REVERT: A 102 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: B 1124 GLU cc_start: 0.7080 (tp30) cc_final: 0.6765 (tp30) REVERT: B 1225 TYR cc_start: 0.8216 (t80) cc_final: 0.7817 (t80) REVERT: B 1304 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7365 (mtmt) REVERT: C 55 ARG cc_start: 0.6019 (OUTLIER) cc_final: 0.5669 (pmm150) REVERT: C 105 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7118 (mt-10) outliers start: 10 outliers final: 4 residues processed: 64 average time/residue: 0.7222 time to fit residues: 47.7936 Evaluate side-chains 68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 1296 GLU Chi-restraints excluded: chain B residue 1304 LYS Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1229 GLN B1301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134949 restraints weight = 5155.868| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.48 r_work: 0.3383 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4933 Z= 0.115 Angle : 0.466 4.797 6654 Z= 0.250 Chirality : 0.038 0.126 743 Planarity : 0.003 0.045 850 Dihedral : 4.328 22.661 636 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.22 % Allowed : 23.48 % Favored : 74.31 % 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 aren not related in a simple way. whole: 0.74 (0.35), residues: 589 helix: 1.25 (0.30), residues: 309 sheet: 0.19 (0.63), residues: 61 loop : -0.40 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1308 TYR 0.017 0.001 TYR C 62 PHE 0.012 0.001 PHE C 239 TRP 0.009 0.001 TRP B1198 HIS 0.003 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4933) covalent geometry : angle 0.46573 ( 6654) hydrogen bonds : bond 0.03594 ( 240) hydrogen bonds : angle 4.23031 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.209 Fit side-chains REVERT: A 11 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7936 (ttmt) REVERT: A 33 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8490 (t) REVERT: A 102 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8116 (mtp) REVERT: B 1124 GLU cc_start: 0.7070 (tp30) cc_final: 0.6755 (tp30) REVERT: B 1225 TYR cc_start: 0.8183 (t80) cc_final: 0.7783 (t80) REVERT: B 1304 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7368 (mtmt) REVERT: C 55 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.5691 (pmm150) REVERT: C 105 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7021 (mm-30) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 0.6967 time to fit residues: 46.2186 Evaluate side-chains 66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain B residue 1296 GLU Chi-restraints excluded: chain B residue 1304 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B1301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135729 restraints weight = 5012.283| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.41 r_work: 0.3400 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4933 Z= 0.115 Angle : 0.469 5.054 6654 Z= 0.251 Chirality : 0.038 0.133 743 Planarity : 0.003 0.044 850 Dihedral : 4.302 23.019 636 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.22 % Allowed : 23.66 % Favored : 74.12 % 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 aren not related in a simple way. whole: 0.83 (0.35), residues: 589 helix: 1.31 (0.30), residues: 309 sheet: 0.29 (0.63), residues: 61 loop : -0.38 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1308 TYR 0.017 0.001 TYR C 62 PHE 0.012 0.001 PHE C 239 TRP 0.008 0.001 TRP B1198 HIS 0.003 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4933) covalent geometry : angle 0.46943 ( 6654) hydrogen bonds : bond 0.03572 ( 240) hydrogen bonds : angle 4.20214 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.206 Fit side-chains REVERT: A 33 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8494 (t) REVERT: A 102 MET cc_start: 0.8440 (mtp) cc_final: 0.8126 (mtp) REVERT: B 1124 GLU cc_start: 0.7091 (tp30) cc_final: 0.6784 (tp30) REVERT: B 1225 TYR cc_start: 0.8209 (t80) cc_final: 0.7719 (t80) REVERT: B 1304 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7428 (mtmt) REVERT: C 55 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.5710 (pmm150) REVERT: C 105 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6976 (mm-30) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.7025 time to fit residues: 49.4640 Evaluate side-chains 66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 1127 MET Chi-restraints excluded: chain B residue 1304 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133847 restraints weight = 5093.364| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.47 r_work: 0.3373 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4933 Z= 0.149 Angle : 0.520 7.520 6654 Z= 0.273 Chirality : 0.040 0.160 743 Planarity : 0.004 0.044 850 Dihedral : 4.445 22.783 636 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.66 % Allowed : 24.40 % Favored : 73.94 % 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 aren not related in a simple way. whole: 0.70 (0.35), residues: 589 helix: 1.16 (0.30), residues: 309 sheet: 0.27 (0.63), residues: 61 loop : -0.38 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 66 TYR 0.018 0.002 TYR C 62 PHE 0.014 0.001 PHE C 239 TRP 0.009 0.001 TRP B1198 HIS 0.004 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4933) covalent geometry : angle 0.51991 ( 6654) hydrogen bonds : bond 0.03947 ( 240) hydrogen bonds : angle 4.26062 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.214 Fit side-chains REVERT: A 33 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8486 (t) REVERT: A 102 MET cc_start: 0.8450 (mtp) cc_final: 0.8122 (mtp) REVERT: B 1124 GLU cc_start: 0.7103 (tp30) cc_final: 0.6790 (tp30) REVERT: B 1225 TYR cc_start: 0.8225 (t80) cc_final: 0.7828 (t80) REVERT: B 1304 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7379 (mtmt) REVERT: C 55 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5727 (pmm150) REVERT: C 105 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7013 (mm-30) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.7358 time to fit residues: 46.4640 Evaluate side-chains 64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 1127 MET Chi-restraints excluded: chain B residue 1304 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 6 optimal weight: 0.2980 chunk 52 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.135720 restraints weight = 5095.827| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.35 r_work: 0.3416 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4933 Z= 0.125 Angle : 0.494 9.001 6654 Z= 0.261 Chirality : 0.039 0.169 743 Planarity : 0.003 0.045 850 Dihedral : 4.369 22.737 636 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.66 % Allowed : 24.58 % Favored : 73.75 % 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 aren not related in a simple way. whole: 0.80 (0.35), residues: 589 helix: 1.26 (0.30), residues: 309 sheet: 0.35 (0.63), residues: 61 loop : -0.37 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1308 TYR 0.017 0.001 TYR C 62 PHE 0.012 0.001 PHE C 239 TRP 0.008 0.001 TRP B1198 HIS 0.003 0.001 HIS B1212 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4933) covalent geometry : angle 0.49374 ( 6654) hydrogen bonds : bond 0.03709 ( 240) hydrogen bonds : angle 4.23357 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.70 seconds wall clock time: 37 minutes 5.32 seconds (2225.32 seconds total)