Starting phenix.real_space_refine on Fri Oct 23 00:01:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t9r_55728/10_2026/9t9r_55728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t9r_55728/10_2026/9t9r_55728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t9r_55728/10_2026/9t9r_55728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t9r_55728/10_2026/9t9r_55728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t9r_55728/10_2026/9t9r_55728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t9r_55728/10_2026/9t9r_55728.map" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4323 2.51 5 N 1174 2.21 5 O 1360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6877 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 676 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 2 Chain: "H" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1289 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain breaks: 4 Chain: "G" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 4 Chain: "F" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1698 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 421 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain breaks: 3 Chain: "B" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 628 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain breaks: 1 Chain: "C" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 534 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain breaks: 4 Chain: "D" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 523 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain breaks: 3 Time building chain proxies: 1.46, per 1000 atoms: 0.21 Number of scatterers: 6877 At special positions: 0 Unit cell: (77.72, 136.68, 76.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1360 8.00 N 1174 7.00 C 4323 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: 0.50 Conformation dependent library (CDL) restraints added in 370.0 milliseconds 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 19 sheets defined 2.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 152 through 158 removed outlier: 3.846A pdb=" N HIS H 156 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 158 Processing helix chain 'F' and resid 153 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.798A pdb=" N ILE B 150 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 122 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 13 through 18 removed outlier: 3.827A pdb=" N SER G 15 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL H 16 " --> pdb=" O SER G 15 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR G 17 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL H 18 " --> pdb=" O THR G 17 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR F 12 " --> pdb=" O TYR H 13 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N SER H 15 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN F 14 " --> pdb=" O SER H 15 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N THR H 17 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 93 through 96 Processing sheet with id=AA6, first strand: chain 'H' and resid 161 through 163 removed outlier: 4.226A pdb=" N PHE H 162 " --> pdb=" O LEU H 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 178 through 183 removed outlier: 6.695A pdb=" N LYS H 211 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL H 207 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 213 " --> pdb=" O PHE H 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.730A pdb=" N GLY F 70 " --> pdb=" O ASP F 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AB2, first strand: chain 'F' and resid 93 through 100 removed outlier: 6.770A pdb=" N ARG F 93 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU F 138 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN F 95 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE F 136 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR F 134 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS F 132 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 161 through 164 removed outlier: 4.643A pdb=" N ILE F 229 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 179 through 180 removed outlier: 4.053A pdb=" N VAL F 180 " --> pdb=" O PHE F 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 198 through 199 removed outlier: 4.330A pdb=" N GLY F 224 " --> pdb=" O TYR F 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 96 through 100 removed outlier: 3.713A pdb=" N SER E 99 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E 174 " --> pdb=" O PHE E 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB8, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AB9, first strand: chain 'D' and resid 109 through 111 removed outlier: 7.117A pdb=" N ILE D 158 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.745A pdb=" N ILE D 150 " --> pdb=" O VAL D 122 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 204 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: 1.01 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1190 1.31 - 1.43: 1703 1.43 - 1.56: 4042 1.56 - 1.68: 4 1.68 - 1.81: 34 Bond restraints: 6973 Sorted by residual: bond pdb=" N PRO B 145 " pdb=" CA PRO B 145 " ideal model delta sigma weight residual 1.465 1.577 -0.112 1.17e-02 7.31e+03 9.17e+01 bond pdb=" CG PRO B 145 " pdb=" CD PRO B 145 " ideal model delta sigma weight residual 1.503 1.182 0.321 3.40e-02 8.65e+02 8.92e+01 bond pdb=" CB PRO B 145 " pdb=" CG PRO B 145 " ideal model delta sigma weight residual 1.492 1.213 0.279 5.00e-02 4.00e+02 3.11e+01 bond pdb=" N PRO B 145 " pdb=" CD PRO B 145 " ideal model delta sigma weight residual 1.473 1.412 0.061 1.40e-02 5.10e+03 1.90e+01 bond pdb=" CA PRO B 145 " pdb=" C PRO B 145 " ideal model delta sigma weight residual 1.526 1.481 0.045 1.13e-02 7.83e+03 1.55e+01 ... (remaining 6968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.76: 9424 14.76 - 29.52: 0 29.52 - 44.28: 2 44.28 - 59.04: 0 59.04 - 73.80: 1 Bond angle restraints: 9427 Sorted by residual: angle pdb=" N PRO B 145 " pdb=" CD PRO B 145 " pdb=" CG PRO B 145 " ideal model delta sigma weight residual 103.20 67.94 35.26 1.50e+00 4.44e-01 5.53e+02 angle pdb=" CB PRO B 145 " pdb=" CG PRO B 145 " pdb=" CD PRO B 145 " ideal model delta sigma weight residual 106.10 179.90 -73.80 3.20e+00 9.77e-02 5.32e+02 angle pdb=" CA PRO B 145 " pdb=" CB PRO B 145 " pdb=" CG PRO B 145 " ideal model delta sigma weight residual 104.50 72.15 32.35 1.90e+00 2.77e-01 2.90e+02 angle pdb=" CA PRO E 113 " pdb=" N PRO E 113 " pdb=" CD PRO E 113 " ideal model delta sigma weight residual 112.00 100.54 11.46 1.40e+00 5.10e-01 6.70e+01 angle pdb=" C VAL B 144 " pdb=" CA VAL B 144 " pdb=" CB VAL B 144 " ideal model delta sigma weight residual 111.00 104.70 6.30 9.80e-01 1.04e+00 4.13e+01 ... (remaining 9422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 3789 24.83 - 49.65: 371 49.65 - 74.48: 40 74.48 - 99.30: 5 99.30 - 124.13: 2 Dihedral angle restraints: 4207 sinusoidal: 1658 harmonic: 2549 Sorted by residual: dihedral pdb=" N PRO B 145 " pdb=" CG PRO B 145 " pdb=" CD PRO B 145 " pdb=" CB PRO B 145 " ideal model delta sinusoidal sigma weight residual -30.00 -132.23 102.23 1 1.50e+01 4.44e-03 5.17e+01 dihedral pdb=" CA PRO B 145 " pdb=" CB PRO B 145 " pdb=" CG PRO B 145 " pdb=" CD PRO B 145 " ideal model delta sinusoidal sigma weight residual -38.00 -162.13 124.13 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" CA TYR G 50 " pdb=" C TYR G 50 " pdb=" N PHE G 51 " pdb=" CA PHE G 51 " ideal model delta harmonic sigma weight residual 180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 4204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 892 0.064 - 0.127: 180 0.127 - 0.191: 17 0.191 - 0.255: 4 0.255 - 0.319: 1 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CB VAL F 207 " pdb=" CA VAL F 207 " pdb=" CG1 VAL F 207 " pdb=" CG2 VAL F 207 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CG LEU H 28 " pdb=" CB LEU H 28 " pdb=" CD1 LEU H 28 " pdb=" CD2 LEU H 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU G 215 " pdb=" CB LEU G 215 " pdb=" CD1 LEU G 215 " pdb=" CD2 LEU G 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1091 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 142 " -0.089 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO A 143 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 112 " 0.083 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO E 113 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO E 113 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 113 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 123 " 0.063 5.00e-02 4.00e+02 9.47e-02 1.43e+01 pdb=" N PRO B 124 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.052 5.00e-02 4.00e+02 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 183 2.66 - 3.22: 6462 3.22 - 3.78: 9584 3.78 - 4.34: 12561 4.34 - 4.90: 20778 Nonbonded interactions: 49568 Sorted by model distance: nonbonded pdb=" OE1 GLN G 200 " pdb=" OG SER G 221 " model vdw 2.099 3.040 nonbonded pdb=" NE ARG H 90 " pdb=" OE2 GLU H 140 " model vdw 2.110 3.120 nonbonded pdb=" OG SER G 172 " pdb=" OG1 THR G 222 " model vdw 2.172 3.040 nonbonded pdb=" O ASN G 167 " pdb=" NE2 GLN F 206 " model vdw 2.208 3.120 nonbonded pdb=" N GLN D 155 " pdb=" OE1 GLN D 155 " model vdw 2.212 3.120 ... (remaining 49563 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 90 through 130 or resid 143 through 180)) selection = (chain 'B' and (resid 90 through 130 or resid 143 through 180)) } ncs_group { reference = (chain 'G' and (resid 8 through 58 or resid 81 through 167 or resid 177 through \ 218 or resid 231 through 235)) selection = (chain 'H' and (resid 8 through 36 or resid 46 through 57 or resid 76 or resid 8 \ 1 through 87 or resid 137 through 228 or resid 231 through 235)) } 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: 2.880 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: 0.030 Set scattering table: 0.020 Process input model: 7.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.007 0.321 6973 Z= 0.276 Angle : 1.212 73.804 9427 Z= 0.585 Chirality : 0.050 0.319 1094 Planarity : 0.008 0.130 1227 Dihedral : 18.268 124.128 2553 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.81 % Favored : 86.83 % Rotamer: Outliers : 0.90 % Allowed : 35.57 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.27), residues: 835 helix: -3.03 (1.09), residues: 18 sheet: -0.98 (0.43), residues: 179 loop : -2.44 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 90 TYR 0.058 0.002 TYR H 50 PHE 0.048 0.002 PHE A 179 TRP 0.011 0.002 TRP F 55 HIS 0.003 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.28 ( 6973) covalent geometry : angle 1.21214 / 0.59 ( 9427) hydrogen bonds : bond 0.31144 / 19.20 ( 86) hydrogen bonds : angle 12.30366 / 7.98 ( 204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 0.233 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 217 average time/residue: 0.0798 time to fit residues: 23.0286 Evaluate side-chains 216 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 212 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0060 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN C 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139558 restraints weight = 10801.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141688 restraints weight = 6779.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142653 restraints weight = 4110.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143191 restraints weight = 3133.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143949 restraints weight = 2652.145| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6973 Z= 0.137 Angle : 0.665 16.868 9427 Z= 0.342 Chirality : 0.047 0.206 1094 Planarity : 0.005 0.075 1227 Dihedral : 5.322 31.022 939 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.62 % Favored : 88.02 % Rotamer: Outliers : 7.35 % Allowed : 29.38 % Favored : 63.27 % 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: -3.02 (0.27), residues: 835 helix: -2.74 (1.17), residues: 18 sheet: -0.95 (0.44), residues: 163 loop : -2.49 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 90 TYR 0.020 0.002 TYR F 50 PHE 0.018 0.001 PHE A 179 TRP 0.003 0.001 TRP H 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 6973) covalent geometry : angle 0.66470 / 0.34 ( 9427) hydrogen bonds : bond 0.04411 / 2.69 ( 86) hydrogen bonds : angle 8.08337 / 5.11 ( 204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 103 VAL cc_start: 0.9177 (t) cc_final: 0.8935 (p) REVERT: H 55 TRP cc_start: 0.7874 (OUTLIER) cc_final: 0.7234 (m-90) REVERT: F 183 GLN cc_start: 0.8062 (mm110) cc_final: 0.7703 (mm110) REVERT: E 179 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7313 (t80) REVERT: B 100 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8529 (tm-30) REVERT: B 155 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7264 (tm130) outliers start: 57 outliers final: 30 residues processed: 260 average time/residue: 0.0714 time to fit residues: 24.7455 Evaluate side-chains 243 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 179 PHE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [8, 2, 32, 18, 56, 20, 27, 30, 82, 28, 69] chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 28 optimal weight: 0.0870 chunk 69 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139768 restraints weight = 10769.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141946 restraints weight = 6076.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143484 restraints weight = 3968.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144440 restraints weight = 2864.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145205 restraints weight = 2267.864| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6973 Z= 0.141 Angle : 0.614 7.321 9427 Z= 0.317 Chirality : 0.046 0.187 1094 Planarity : 0.004 0.057 1227 Dihedral : 5.150 29.590 935 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.10 % Favored : 87.54 % Rotamer: Outliers : 7.99 % Allowed : 29.12 % Favored : 62.89 % 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: -3.00 (0.27), residues: 835 helix: -2.81 (1.15), residues: 18 sheet: -1.01 (0.44), residues: 166 loop : -2.46 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 115 TYR 0.019 0.002 TYR F 50 PHE 0.012 0.001 PHE G 51 TRP 0.003 0.001 TRP H 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 6973) covalent geometry : angle 0.61439 / 0.32 ( 9427) hydrogen bonds : bond 0.03851 / 2.24 ( 86) hydrogen bonds : angle 7.33820 / 4.62 ( 204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 218 time to evaluate : 0.267 Fit side-chains REVERT: A 68 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: A 103 VAL cc_start: 0.9170 (t) cc_final: 0.8954 (p) REVERT: H 55 TRP cc_start: 0.7605 (OUTLIER) cc_final: 0.6839 (m-90) REVERT: G 11 VAL cc_start: 0.8375 (m) cc_final: 0.8129 (m) REVERT: F 114 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7611 (mp0) REVERT: F 216 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7329 (mmmt) REVERT: B 100 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8540 (tm-30) REVERT: B 155 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7109 (tm130) REVERT: D 179 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6646 (t80) outliers start: 62 outliers final: 45 residues processed: 255 average time/residue: 0.0697 time to fit residues: 23.9014 Evaluate side-chains 261 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [41, 76, 60, 23, 79, 31, 64, 2, 10, 80, 71] chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** 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 = 0.3632 r_free = 0.3632 target = 0.144555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133215 restraints weight = 11108.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135337 restraints weight = 6423.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136740 restraints weight = 4227.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137585 restraints weight = 3088.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138334 restraints weight = 2483.751| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6973 Z= 0.270 Angle : 0.730 7.462 9427 Z= 0.377 Chirality : 0.049 0.156 1094 Planarity : 0.005 0.053 1227 Dihedral : 5.975 42.105 935 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 15.09 % Favored : 84.55 % Rotamer: Outliers : 10.05 % Allowed : 28.22 % Favored : 61.73 % 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: -3.04 (0.27), residues: 835 helix: -2.84 (1.13), residues: 18 sheet: -0.92 (0.42), residues: 182 loop : -2.55 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 115 TYR 0.025 0.003 TYR G 50 PHE 0.017 0.002 PHE G 51 TRP 0.006 0.002 TRP F 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.27 ( 6973) covalent geometry : angle 0.72956 / 0.38 ( 9427) hydrogen bonds : bond 0.03923 / 2.27 ( 86) hydrogen bonds : angle 7.66759 / 4.89 ( 204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 215 time to evaluate : 0.230 Fit side-chains REVERT: A 99 SER cc_start: 0.8704 (p) cc_final: 0.8455 (t) REVERT: H 45 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7669 (pp) REVERT: G 11 VAL cc_start: 0.8592 (m) cc_final: 0.8271 (m) REVERT: F 50 TYR cc_start: 0.8231 (m-80) cc_final: 0.7827 (m-80) REVERT: B 155 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7601 (tm130) REVERT: D 179 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6635 (t80) outliers start: 78 outliers final: 63 residues processed: 261 average time/residue: 0.0716 time to fit residues: 25.0419 Evaluate side-chains 274 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [25, 11, 68, 79, 22, 3, 49, 32, 30, 41, 60] chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 0.0870 chunk 79 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 156 HIS G 206 GLN F 156 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139248 restraints weight = 10898.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141354 restraints weight = 7327.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142772 restraints weight = 4330.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143225 restraints weight = 3056.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143566 restraints weight = 2627.848| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6973 Z= 0.145 Angle : 0.635 8.133 9427 Z= 0.327 Chirality : 0.047 0.263 1094 Planarity : 0.004 0.051 1227 Dihedral : 5.381 40.047 935 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.10 % Favored : 87.54 % Rotamer: Outliers : 8.63 % Allowed : 30.15 % Favored : 61.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.27), residues: 835 helix: -2.77 (1.16), residues: 18 sheet: -0.93 (0.43), residues: 179 loop : -2.48 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 115 TYR 0.021 0.002 TYR F 147 PHE 0.020 0.001 PHE G 51 TRP 0.002 0.001 TRP H 55 HIS 0.003 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6973) covalent geometry : angle 0.63458 / 0.33 ( 9427) hydrogen bonds : bond 0.03299 / 1.87 ( 86) hydrogen bonds : angle 6.94272 / 4.38 ( 204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 0.199 Fit side-chains REVERT: A 99 SER cc_start: 0.8644 (p) cc_final: 0.8392 (t) REVERT: A 103 VAL cc_start: 0.9025 (t) cc_final: 0.8761 (p) REVERT: H 186 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8272 (tm-30) REVERT: G 150 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8308 (mt) REVERT: F 50 TYR cc_start: 0.8099 (m-80) cc_final: 0.7638 (m-10) REVERT: B 100 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8559 (tm-30) REVERT: B 155 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7142 (tm130) REVERT: D 179 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6674 (t80) outliers start: 67 outliers final: 53 residues processed: 255 average time/residue: 0.0749 time to fit residues: 25.6832 Evaluate side-chains 264 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [78, 48, 22, 43, 27, 40, 39, 57, 56, 34, 81] chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.151520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140264 restraints weight = 10870.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142411 restraints weight = 6183.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143819 restraints weight = 4060.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144785 restraints weight = 2954.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145495 restraints weight = 2328.746| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6973 Z= 0.134 Angle : 0.623 9.127 9427 Z= 0.319 Chirality : 0.047 0.269 1094 Planarity : 0.004 0.049 1227 Dihedral : 5.181 37.115 935 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.93 % Favored : 86.83 % Rotamer: Outliers : 9.02 % Allowed : 30.15 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.27), residues: 835 helix: -2.76 (1.14), residues: 18 sheet: -0.87 (0.43), residues: 179 loop : -2.43 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 115 TYR 0.013 0.001 TYR H 199 PHE 0.022 0.001 PHE G 51 TRP 0.002 0.001 TRP H 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 6973) covalent geometry : angle 0.62310 / 0.32 ( 9427) hydrogen bonds : bond 0.03103 / 1.76 ( 86) hydrogen bonds : angle 6.75357 / 4.27 ( 204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 99 SER cc_start: 0.8650 (p) cc_final: 0.8425 (t) REVERT: A 103 VAL cc_start: 0.9013 (t) cc_final: 0.8735 (p) REVERT: H 55 TRP cc_start: 0.7687 (OUTLIER) cc_final: 0.6986 (m-90) REVERT: G 150 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8320 (mt) REVERT: F 50 TYR cc_start: 0.8110 (m-80) cc_final: 0.7639 (m-10) REVERT: F 114 GLU cc_start: 0.8142 (mp0) cc_final: 0.7664 (mp0) REVERT: F 183 GLN cc_start: 0.8136 (mm110) cc_final: 0.7567 (mm110) REVERT: B 100 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8594 (tm-30) REVERT: B 155 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7170 (tm130) REVERT: D 179 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6704 (t80) outliers start: 70 outliers final: 56 residues processed: 258 average time/residue: 0.0745 time to fit residues: 25.8907 Evaluate side-chains 270 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [26, 71, 13, 35, 40, 20, 68, 21, 2, 36, 55] chunk 26 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140284 restraints weight = 10824.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142384 restraints weight = 6165.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143794 restraints weight = 4048.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144784 restraints weight = 2955.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145394 restraints weight = 2325.901| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6973 Z= 0.146 Angle : 0.637 9.986 9427 Z= 0.326 Chirality : 0.047 0.273 1094 Planarity : 0.004 0.049 1227 Dihedral : 5.183 37.828 935 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.98 % Favored : 87.78 % Rotamer: Outliers : 10.18 % Allowed : 29.38 % Favored : 60.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.27), residues: 835 helix: -2.62 (1.18), residues: 18 sheet: -0.84 (0.43), residues: 177 loop : -2.40 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 115 TYR 0.014 0.001 TYR H 199 PHE 0.022 0.001 PHE G 51 TRP 0.003 0.001 TRP F 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6973) covalent geometry : angle 0.63654 / 0.33 ( 9427) hydrogen bonds : bond 0.03140 / 1.75 ( 86) hydrogen bonds : angle 6.67383 / 4.21 ( 204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 223 time to evaluate : 0.266 Fit side-chains REVERT: A 99 SER cc_start: 0.8656 (p) cc_final: 0.8433 (t) REVERT: A 103 VAL cc_start: 0.9007 (t) cc_final: 0.8769 (p) REVERT: A 105 LYS cc_start: 0.8553 (tptm) cc_final: 0.8342 (tptp) REVERT: H 55 TRP cc_start: 0.7710 (OUTLIER) cc_final: 0.6903 (m-90) REVERT: G 150 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8329 (mt) REVERT: F 50 TYR cc_start: 0.8082 (m-80) cc_final: 0.7660 (m-10) REVERT: F 114 GLU cc_start: 0.8155 (mp0) cc_final: 0.7709 (mp0) REVERT: F 174 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7422 (mp) REVERT: F 183 GLN cc_start: 0.8094 (mm110) cc_final: 0.7553 (mm110) REVERT: B 100 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8620 (tm-30) REVERT: B 125 LEU cc_start: 0.8576 (mt) cc_final: 0.8112 (mt) REVERT: B 155 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7246 (tm130) REVERT: D 179 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6670 (t80) outliers start: 79 outliers final: 61 residues processed: 269 average time/residue: 0.0736 time to fit residues: 26.6875 Evaluate side-chains 281 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [16, 41, 69, 1, 37, 45, 55, 11, 75, 23, 78] chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN B 126 ASN B 168 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.150444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139310 restraints weight = 10896.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141448 restraints weight = 6247.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142829 restraints weight = 4092.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143825 restraints weight = 2987.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144430 restraints weight = 2353.088| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6973 Z= 0.164 Angle : 0.676 10.890 9427 Z= 0.342 Chirality : 0.048 0.293 1094 Planarity : 0.004 0.048 1227 Dihedral : 5.279 38.431 935 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.81 % Favored : 86.95 % Rotamer: Outliers : 9.92 % Allowed : 30.67 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.27), residues: 835 helix: -2.51 (1.21), residues: 18 sheet: -0.91 (0.44), residues: 163 loop : -2.41 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 115 TYR 0.016 0.001 TYR H 199 PHE 0.022 0.001 PHE G 51 TRP 0.004 0.001 TRP F 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 6973) covalent geometry : angle 0.67606 / 0.34 ( 9427) hydrogen bonds : bond 0.03124 / 1.74 ( 86) hydrogen bonds : angle 6.67104 / 4.21 ( 204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 217 time to evaluate : 0.285 Fit side-chains REVERT: A 99 SER cc_start: 0.8717 (p) cc_final: 0.8426 (t) REVERT: A 103 VAL cc_start: 0.9027 (t) cc_final: 0.8820 (p) REVERT: H 55 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6996 (m-90) REVERT: G 150 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8303 (mt) REVERT: G 222 THR cc_start: 0.8576 (t) cc_final: 0.8276 (t) REVERT: F 50 TYR cc_start: 0.8215 (m-80) cc_final: 0.7825 (m-10) REVERT: F 114 GLU cc_start: 0.8080 (mp0) cc_final: 0.7598 (mp0) REVERT: F 174 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7456 (mp) REVERT: B 125 LEU cc_start: 0.8597 (mt) cc_final: 0.8103 (mt) REVERT: B 155 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7278 (tm130) REVERT: D 179 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6613 (t80) outliers start: 77 outliers final: 68 residues processed: 262 average time/residue: 0.0706 time to fit residues: 24.9950 Evaluate side-chains 283 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 210 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [0, 30, 73, 50, 48, 24, 45, 22, 28, 52, 8] chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 28 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139939 restraints weight = 10897.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142072 restraints weight = 6189.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143529 restraints weight = 4044.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144526 restraints weight = 2926.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145087 restraints weight = 2293.918| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6973 Z= 0.157 Angle : 0.683 11.436 9427 Z= 0.347 Chirality : 0.048 0.306 1094 Planarity : 0.004 0.048 1227 Dihedral : 5.273 38.927 935 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.10 % Favored : 87.66 % Rotamer: Outliers : 9.41 % Allowed : 30.67 % Favored : 59.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.27), residues: 835 helix: -2.37 (1.26), residues: 18 sheet: -0.91 (0.44), residues: 163 loop : -2.39 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 115 TYR 0.024 0.001 TYR G 50 PHE 0.021 0.001 PHE G 51 TRP 0.004 0.001 TRP F 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 6973) covalent geometry : angle 0.68272 / 0.35 ( 9427) hydrogen bonds : bond 0.03115 / 1.73 ( 86) hydrogen bonds : angle 6.61532 / 4.18 ( 204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 0.242 Fit side-chains REVERT: A 99 SER cc_start: 0.8735 (p) cc_final: 0.8428 (t) REVERT: A 103 VAL cc_start: 0.9013 (t) cc_final: 0.8794 (p) REVERT: H 55 TRP cc_start: 0.7814 (OUTLIER) cc_final: 0.7023 (m-90) REVERT: G 150 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8326 (mt) REVERT: F 50 TYR cc_start: 0.8213 (m-80) cc_final: 0.7809 (m-10) REVERT: F 114 GLU cc_start: 0.7971 (mp0) cc_final: 0.7428 (mp0) REVERT: F 174 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7426 (mp) REVERT: F 183 GLN cc_start: 0.8099 (mm110) cc_final: 0.7643 (mm110) REVERT: B 125 LEU cc_start: 0.8651 (mt) cc_final: 0.8150 (mt) REVERT: B 155 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7253 (tm130) REVERT: D 179 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6636 (t80) outliers start: 73 outliers final: 64 residues processed: 254 average time/residue: 0.0755 time to fit residues: 25.8864 Evaluate side-chains 276 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [43, 45, 32, 51, 4, 50, 6, 23, 3, 55, 46] chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141580 restraints weight = 10801.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143472 restraints weight = 6989.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144948 restraints weight = 4336.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145332 restraints weight = 3120.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145896 restraints weight = 2614.350| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6973 Z= 0.162 Angle : 0.696 12.000 9427 Z= 0.353 Chirality : 0.048 0.308 1094 Planarity : 0.004 0.048 1227 Dihedral : 5.299 38.535 935 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.46 % Favored : 87.31 % Rotamer: Outliers : 9.41 % Allowed : 31.19 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.27), residues: 835 helix: -2.33 (1.27), residues: 18 sheet: -0.80 (0.46), residues: 153 loop : -2.36 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 115 TYR 0.021 0.001 TYR G 50 PHE 0.020 0.001 PHE G 51 TRP 0.005 0.001 TRP F 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 6973) covalent geometry : angle 0.69576 / 0.35 ( 9427) hydrogen bonds : bond 0.03033 / 1.68 ( 86) hydrogen bonds : angle 6.60169 / 4.18 ( 204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 0.258 Fit side-chains REVERT: A 99 SER cc_start: 0.8758 (p) cc_final: 0.8443 (t) REVERT: A 103 VAL cc_start: 0.9035 (t) cc_final: 0.8815 (p) REVERT: H 12 THR cc_start: 0.7917 (m) cc_final: 0.7704 (t) REVERT: H 55 TRP cc_start: 0.7827 (OUTLIER) cc_final: 0.7057 (m-90) REVERT: G 150 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8334 (mt) REVERT: F 50 TYR cc_start: 0.8202 (m-80) cc_final: 0.7844 (m-80) REVERT: F 114 GLU cc_start: 0.7984 (mp0) cc_final: 0.7439 (mp0) REVERT: F 174 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7395 (mp) REVERT: F 183 GLN cc_start: 0.8127 (mm110) cc_final: 0.7667 (mm110) REVERT: B 125 LEU cc_start: 0.8656 (mt) cc_final: 0.8115 (mt) REVERT: B 155 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7246 (tm130) REVERT: D 179 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6723 (t80) outliers start: 73 outliers final: 66 residues processed: 256 average time/residue: 0.0701 time to fit residues: 24.4374 Evaluate side-chains 281 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 210 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 10 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 179 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: [61, 53, 16, 14, 41, 76, 40, 55, 64, 72, 30] chunk 61 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** 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 = 0.3694 r_free = 0.3694 target = 0.149743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139773 restraints weight = 10867.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141788 restraints weight = 7037.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143319 restraints weight = 4276.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143631 restraints weight = 3024.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143747 restraints weight = 2592.025| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6973 Z= 0.186 Angle : 0.716 12.027 9427 Z= 0.362 Chirality : 0.048 0.310 1094 Planarity : 0.004 0.048 1227 Dihedral : 5.517 40.933 935 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.17 % Favored : 86.59 % Rotamer: Outliers : 9.54 % Allowed : 31.06 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.27), residues: 835 helix: -2.37 (1.24), residues: 18 sheet: -0.96 (0.45), residues: 155 loop : -2.39 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 115 TYR 0.023 0.002 TYR G 50 PHE 0.020 0.002 PHE B 170 TRP 0.006 0.001 TRP F 55 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 6973) covalent geometry : angle 0.71556 / 0.36 ( 9427) hydrogen bonds : bond 0.03162 / 1.74 ( 86) hydrogen bonds : angle 6.70816 / 4.25 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1238.85 seconds wall clock time: 22 minutes 9.39 seconds (1329.39 seconds total)