Starting phenix.real_space_refine on Wed Sep 17 08:32:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xej_38291/09_2025/8xej_38291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xej_38291/09_2025/8xej_38291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xej_38291/09_2025/8xej_38291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xej_38291/09_2025/8xej_38291.map" model { file = "/net/cci-nas-00/data/ceres_data/8xej_38291/09_2025/8xej_38291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xej_38291/09_2025/8xej_38291.cif" } resolution = 3.66 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 29 5.16 5 C 4640 2.51 5 N 1173 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7153 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1032 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2888 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain breaks: 1 Chain: "H" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1553 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1626 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 207} Chain: "X" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'DLP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.29 Number of scatterers: 7153 At special positions: 0 Unit cell: (87.4742, 115.811, 118.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 1 15.00 O 1310 8.00 N 1173 7.00 C 4640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 185 " distance=2.02 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 81 " - pdb=" SG CYS L 175 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.03 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: 0.62 Conformation dependent library (CDL) restraints added in 392.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 40.6% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 209 through 230 removed outlier: 3.737A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 41 Processing helix chain 'X' and resid 42 through 71 removed outlier: 4.466A pdb=" N ALA X 46 " --> pdb=" O ARG X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 91 removed outlier: 3.787A pdb=" N LEU X 87 " --> pdb=" O ARG X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 93 through 112 Processing helix chain 'X' and resid 116 through 157 removed outlier: 4.926A pdb=" N ALA X 143 " --> pdb=" O PHE X 139 " (cutoff:3.500A) Proline residue: X 144 - end of helix Processing helix chain 'X' and resid 160 through 188 Processing helix chain 'X' and resid 195 through 225 Proline residue: X 213 - end of helix Processing helix chain 'X' and resid 228 through 247 Processing helix chain 'X' and resid 257 through 272 removed outlier: 4.280A pdb=" N TYR X 261 " --> pdb=" O SER X 257 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE X 271 " --> pdb=" O THR X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 283 through 306 Processing helix chain 'X' and resid 315 through 340 Proline residue: X 321 - end of helix Processing helix chain 'X' and resid 371 through 382 Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.645A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 200 through 203 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.519A pdb=" N ALA L 84 " --> pdb=" O CYS L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 125 through 132 Processing helix chain 'L' and resid 187 through 193 Processing sheet with id=AA1, first strand: chain 'B' and resid 107 through 109 Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.870A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLN B 182 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP B 136 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.799A pdb=" N ALA H 32 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET H 33 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE H 49 " --> pdb=" O MET H 33 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP H 35 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.215A pdb=" N ILE H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 119 through 123 removed outlier: 6.146A pdb=" N TYR H 175 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 119 through 123 removed outlier: 6.146A pdb=" N TYR H 175 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER H 176 " --> pdb=" O VAL H 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 150 through 153 Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 15 removed outlier: 6.397A pdb=" N VAL L 12 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS L 111 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA L 14 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA L 85 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.530A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 157 through 158 removed outlier: 3.624A pdb=" N LYS L 211 " --> pdb=" O CYS L 198 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1242 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: 1.13 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1295 1.33 - 1.45: 1984 1.45 - 1.58: 4024 1.58 - 1.70: 2 1.70 - 1.82: 38 Bond restraints: 7343 Sorted by residual: bond pdb=" N PCA H 1 " pdb=" CD PCA H 1 " ideal model delta sigma weight residual 1.345 1.462 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C4 DLP X 501 " pdb=" O4P DLP X 501 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 DLP X 501 " pdb=" O3P DLP X 501 " ideal model delta sigma weight residual 1.409 1.452 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" O4P DLP X 501 " pdb=" P DLP X 501 " ideal model delta sigma weight residual 1.649 1.606 0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" C17 DLP X 501 " pdb=" C18 DLP X 501 " ideal model delta sigma weight residual 1.530 1.497 0.033 2.00e-02 2.50e+03 2.65e+00 ... (remaining 7338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 9705 2.17 - 4.35: 267 4.35 - 6.52: 28 6.52 - 8.70: 7 8.70 - 10.87: 4 Bond angle restraints: 10011 Sorted by residual: angle pdb=" N GLY H 98 " pdb=" CA GLY H 98 " pdb=" C GLY H 98 " ideal model delta sigma weight residual 112.37 102.63 9.74 1.84e+00 2.95e-01 2.80e+01 angle pdb=" C PRO X 190 " pdb=" N SER X 191 " pdb=" CA SER X 191 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" N ALA H 97 " pdb=" CA ALA H 97 " pdb=" C ALA H 97 " ideal model delta sigma weight residual 107.23 99.72 7.51 1.67e+00 3.59e-01 2.02e+01 angle pdb=" N PRO X 190 " pdb=" CA PRO X 190 " pdb=" C PRO X 190 " ideal model delta sigma weight residual 111.21 117.82 -6.61 1.59e+00 3.96e-01 1.73e+01 angle pdb=" C CYS X 346 " pdb=" CA CYS X 346 " pdb=" CB CYS X 346 " ideal model delta sigma weight residual 115.89 110.58 5.31 1.32e+00 5.74e-01 1.62e+01 ... (remaining 10006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.89: 4069 22.89 - 45.79: 186 45.79 - 68.68: 38 68.68 - 91.57: 8 91.57 - 114.47: 1 Dihedral angle restraints: 4302 sinusoidal: 1653 harmonic: 2649 Sorted by residual: dihedral pdb=" CB CYS L 81 " pdb=" SG CYS L 81 " pdb=" SG CYS L 175 " pdb=" CB CYS L 175 " ideal model delta sinusoidal sigma weight residual -86.00 -121.64 35.64 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" N DLP X 501 " pdb=" C4 DLP X 501 " pdb=" C5 DLP X 501 " pdb=" O4P DLP X 501 " ideal model delta sinusoidal sigma weight residual 288.95 174.48 114.47 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" CB GLU L 199 " pdb=" CG GLU L 199 " pdb=" CD GLU L 199 " pdb=" OE1 GLU L 199 " ideal model delta sinusoidal sigma weight residual 0.00 86.94 -86.94 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 4299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 732 0.035 - 0.071: 284 0.071 - 0.106: 79 0.106 - 0.141: 36 0.141 - 0.176: 8 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CA ASP B 179 " pdb=" N ASP B 179 " pdb=" C ASP B 179 " pdb=" CB ASP B 179 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" C2 DLP X 501 " pdb=" C1 DLP X 501 " pdb=" C3 DLP X 501 " pdb=" O2 DLP X 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.52 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ALA H 97 " pdb=" N ALA H 97 " pdb=" C ALA H 97 " pdb=" CB ALA H 97 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 1136 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 DLP X 501 " 0.040 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C39 DLP X 501 " -0.038 2.00e-02 2.50e+03 pdb=" C40 DLP X 501 " -0.042 2.00e-02 2.50e+03 pdb=" C41 DLP X 501 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 DLP X 501 " 0.035 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C42 DLP X 501 " -0.038 2.00e-02 2.50e+03 pdb=" C43 DLP X 501 " -0.032 2.00e-02 2.50e+03 pdb=" C44 DLP X 501 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 147 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO H 148 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 148 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 148 " -0.027 5.00e-02 4.00e+02 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1049 2.76 - 3.29: 6662 3.29 - 3.83: 12050 3.83 - 4.36: 13100 4.36 - 4.90: 23687 Nonbonded interactions: 56548 Sorted by model distance: nonbonded pdb=" O GLN L 128 " pdb=" OG SER L 131 " model vdw 2.222 3.040 nonbonded pdb=" O MET B 151 " pdb=" OG SER B 154 " model vdw 2.282 3.040 nonbonded pdb=" O ARG X 183 " pdb=" OG1 THR X 187 " model vdw 2.286 3.040 nonbonded pdb=" NH1 ARG X 134 " pdb=" OD2 ASP X 180 " model vdw 2.300 3.120 nonbonded pdb=" NE2 GLN X 105 " pdb=" OD1 ASP X 119 " model vdw 2.336 3.120 ... (remaining 56543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.470 Find NCS groups from input model: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 : 0.004 0.117 7349 Z= 0.202 Angle : 0.840 10.874 10023 Z= 0.473 Chirality : 0.045 0.176 1139 Planarity : 0.005 0.055 1240 Dihedral : 13.946 114.468 2584 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.64 % Allowed : 8.96 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.28), residues: 903 helix: 2.77 (0.28), residues: 323 sheet: -0.57 (0.30), residues: 252 loop : -2.20 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.017 0.002 TYR L 92 PHE 0.013 0.002 PHE L 120 TRP 0.020 0.002 TRP X 206 HIS 0.006 0.002 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7343) covalent geometry : angle 0.83886 (10011) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.43967 ( 12) hydrogen bonds : bond 0.08505 ( 423) hydrogen bonds : angle 6.29169 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7447 (p0) REVERT: B 123 MET cc_start: 0.8766 (ttp) cc_final: 0.8556 (ttp) REVERT: X 63 PHE cc_start: 0.8015 (m-80) cc_final: 0.7812 (m-80) REVERT: X 79 GLN cc_start: 0.5992 (OUTLIER) cc_final: 0.5678 (mp10) REVERT: X 90 LEU cc_start: 0.7460 (tp) cc_final: 0.6965 (mt) REVERT: X 194 LEU cc_start: 0.5068 (tp) cc_final: 0.4345 (mp) REVERT: X 205 LEU cc_start: 0.8695 (tp) cc_final: 0.8211 (mt) REVERT: X 341 LEU cc_start: 0.8215 (mt) cc_final: 0.6894 (tt) REVERT: H 42 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8830 (mmmm) REVERT: H 111 SER cc_start: 0.7985 (t) cc_final: 0.7746 (m) REVERT: L 62 ARG cc_start: 0.8819 (mtm110) cc_final: 0.8519 (mtm110) REVERT: L 211 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7551 (mmmt) outliers start: 28 outliers final: 7 residues processed: 244 average time/residue: 0.0980 time to fit residues: 30.8201 Evaluate side-chains 129 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 49 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 89 HIS X 92 GLN X 288 HIS X 306 HIS X 317 GLN ** X 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.155015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127729 restraints weight = 10361.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127282 restraints weight = 9776.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127324 restraints weight = 8693.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127455 restraints weight = 8554.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127543 restraints weight = 8051.392| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7349 Z= 0.242 Angle : 0.736 11.900 10023 Z= 0.368 Chirality : 0.044 0.184 1139 Planarity : 0.005 0.044 1240 Dihedral : 7.986 91.912 1048 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.42 % Allowed : 15.97 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.28), residues: 903 helix: 2.69 (0.28), residues: 328 sheet: 0.39 (0.32), residues: 244 loop : -1.56 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 158 TYR 0.019 0.002 TYR L 144 PHE 0.020 0.002 PHE B 159 TRP 0.016 0.002 TRP X 347 HIS 0.007 0.002 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 7343) covalent geometry : angle 0.73389 (10011) SS BOND : bond 0.00591 ( 6) SS BOND : angle 1.75208 ( 12) hydrogen bonds : bond 0.04710 ( 423) hydrogen bonds : angle 5.15274 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8664 (ttp) cc_final: 0.8383 (ttp) REVERT: B 195 GLN cc_start: 0.8020 (pm20) cc_final: 0.7785 (pm20) REVERT: X 79 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.5578 (mp10) REVERT: X 194 LEU cc_start: 0.4948 (tp) cc_final: 0.4480 (mp) REVERT: X 205 LEU cc_start: 0.8787 (tp) cc_final: 0.8336 (mt) REVERT: X 250 ASP cc_start: 0.8098 (m-30) cc_final: 0.7697 (m-30) REVERT: X 286 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8053 (pt) REVERT: X 341 LEU cc_start: 0.8060 (mt) cc_final: 0.6736 (tt) REVERT: H 106 THR cc_start: 0.9283 (p) cc_final: 0.9079 (p) REVERT: H 150 THR cc_start: 0.8488 (t) cc_final: 0.8278 (p) REVERT: L 128 GLN cc_start: 0.7467 (tt0) cc_final: 0.7174 (tt0) outliers start: 34 outliers final: 22 residues processed: 157 average time/residue: 0.0858 time to fit residues: 17.9063 Evaluate side-chains 122 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 322 VAL Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 379 GLN L 151 GLN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128657 restraints weight = 10183.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129275 restraints weight = 8565.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129212 restraints weight = 7666.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129250 restraints weight = 7635.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129273 restraints weight = 7621.973| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7349 Z= 0.140 Angle : 0.658 14.505 10023 Z= 0.317 Chirality : 0.040 0.145 1139 Planarity : 0.004 0.047 1240 Dihedral : 7.436 89.256 1043 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.42 % Allowed : 18.05 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.28), residues: 903 helix: 2.86 (0.28), residues: 328 sheet: 0.74 (0.33), residues: 244 loop : -1.36 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 183 TYR 0.016 0.001 TYR L 98 PHE 0.013 0.001 PHE H 91 TRP 0.015 0.001 TRP X 206 HIS 0.004 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7343) covalent geometry : angle 0.65205 (10011) SS BOND : bond 0.00569 ( 6) SS BOND : angle 2.53592 ( 12) hydrogen bonds : bond 0.03821 ( 423) hydrogen bonds : angle 4.58334 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 GLN cc_start: 0.7937 (pm20) cc_final: 0.7724 (pm20) REVERT: X 79 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5552 (mp10) REVERT: X 160 GLU cc_start: 0.7118 (mp0) cc_final: 0.6840 (mp0) REVERT: X 194 LEU cc_start: 0.4828 (tp) cc_final: 0.4429 (mp) REVERT: X 205 LEU cc_start: 0.8714 (tp) cc_final: 0.8250 (mt) REVERT: X 286 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8047 (pt) REVERT: X 341 LEU cc_start: 0.8038 (mt) cc_final: 0.6611 (tt) REVERT: H 20 THR cc_start: 0.8816 (m) cc_final: 0.8528 (p) REVERT: L 128 GLN cc_start: 0.7375 (tt0) cc_final: 0.7157 (tt0) outliers start: 34 outliers final: 24 residues processed: 140 average time/residue: 0.0741 time to fit residues: 14.3564 Evaluate side-chains 127 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 318 LEU Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126204 restraints weight = 10283.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126543 restraints weight = 8778.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126508 restraints weight = 8223.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126583 restraints weight = 8218.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126604 restraints weight = 8043.463| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7349 Z= 0.154 Angle : 0.666 17.967 10023 Z= 0.314 Chirality : 0.041 0.143 1139 Planarity : 0.004 0.045 1240 Dihedral : 7.255 84.336 1041 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.97 % Allowed : 16.62 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.28), residues: 903 helix: 2.65 (0.28), residues: 330 sheet: 0.77 (0.33), residues: 249 loop : -1.18 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 69 TYR 0.011 0.001 TYR L 177 PHE 0.015 0.001 PHE H 91 TRP 0.015 0.001 TRP X 206 HIS 0.005 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7343) covalent geometry : angle 0.66429 (10011) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.43590 ( 12) hydrogen bonds : bond 0.03731 ( 423) hydrogen bonds : angle 4.45924 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 195 GLN cc_start: 0.7942 (pm20) cc_final: 0.7653 (pm20) REVERT: X 79 GLN cc_start: 0.6236 (OUTLIER) cc_final: 0.5582 (mp10) REVERT: X 205 LEU cc_start: 0.8667 (tp) cc_final: 0.8216 (mt) REVERT: X 259 TRP cc_start: 0.7313 (OUTLIER) cc_final: 0.7108 (p90) REVERT: X 286 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7962 (pt) REVERT: X 341 LEU cc_start: 0.7983 (mt) cc_final: 0.6528 (tt) REVERT: X 380 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8795 (mtpp) REVERT: H 20 THR cc_start: 0.8845 (m) cc_final: 0.8563 (p) REVERT: H 162 VAL cc_start: 0.8665 (t) cc_final: 0.8384 (p) outliers start: 46 outliers final: 29 residues processed: 140 average time/residue: 0.0761 time to fit residues: 14.7610 Evaluate side-chains 126 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 322 VAL Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 0.0040 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 88 optimal weight: 0.0050 overall best weight: 1.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 371 ASN ** L 71 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 = 0.3813 r_free = 0.3813 target = 0.152327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125558 restraints weight = 10406.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125720 restraints weight = 9165.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125701 restraints weight = 8727.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125799 restraints weight = 8383.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125824 restraints weight = 8097.546| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7349 Z= 0.170 Angle : 0.658 17.351 10023 Z= 0.313 Chirality : 0.040 0.146 1139 Planarity : 0.004 0.044 1240 Dihedral : 7.117 80.103 1039 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.71 % Allowed : 17.01 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.29), residues: 903 helix: 2.67 (0.28), residues: 329 sheet: 0.90 (0.33), residues: 249 loop : -1.16 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 146 TYR 0.012 0.002 TYR L 92 PHE 0.015 0.001 PHE H 91 TRP 0.016 0.001 TRP X 206 HIS 0.007 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7343) covalent geometry : angle 0.65691 (10011) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.25488 ( 12) hydrogen bonds : bond 0.03782 ( 423) hydrogen bonds : angle 4.45347 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: B 195 GLN cc_start: 0.7959 (pm20) cc_final: 0.7647 (pm20) REVERT: X 79 GLN cc_start: 0.6136 (OUTLIER) cc_final: 0.5266 (mp10) REVERT: X 205 LEU cc_start: 0.8712 (tp) cc_final: 0.8279 (mt) REVERT: X 259 TRP cc_start: 0.7367 (OUTLIER) cc_final: 0.7134 (p90) REVERT: X 286 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7854 (pt) REVERT: X 341 LEU cc_start: 0.7914 (mt) cc_final: 0.6481 (tt) REVERT: H 20 THR cc_start: 0.8842 (m) cc_final: 0.8546 (p) REVERT: H 85 GLU cc_start: 0.6756 (tp30) cc_final: 0.6538 (tp30) REVERT: H 162 VAL cc_start: 0.8692 (t) cc_final: 0.8458 (p) REVERT: L 146 ARG cc_start: 0.8135 (tmt-80) cc_final: 0.7776 (tpt170) outliers start: 44 outliers final: 34 residues processed: 128 average time/residue: 0.0663 time to fit residues: 12.1267 Evaluate side-chains 127 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 247 GLN Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 322 VAL Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 169 GLU Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122002 restraints weight = 10401.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122525 restraints weight = 8923.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122449 restraints weight = 8128.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122513 restraints weight = 8122.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122529 restraints weight = 8149.614| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7349 Z= 0.185 Angle : 0.665 16.736 10023 Z= 0.318 Chirality : 0.041 0.145 1139 Planarity : 0.004 0.042 1240 Dihedral : 7.086 76.118 1039 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.84 % Allowed : 17.14 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.29), residues: 903 helix: 2.63 (0.28), residues: 329 sheet: 0.92 (0.33), residues: 249 loop : -1.18 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 42 TYR 0.014 0.002 TYR L 92 PHE 0.016 0.001 PHE H 91 TRP 0.015 0.001 TRP X 206 HIS 0.008 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 7343) covalent geometry : angle 0.66331 (10011) SS BOND : bond 0.00573 ( 6) SS BOND : angle 1.32859 ( 12) hydrogen bonds : bond 0.03897 ( 423) hydrogen bonds : angle 4.46459 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: B 195 GLN cc_start: 0.7920 (pm20) cc_final: 0.7659 (pm20) REVERT: X 79 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.5234 (mp10) REVERT: X 132 MET cc_start: 0.7512 (mtm) cc_final: 0.7256 (mtm) REVERT: X 205 LEU cc_start: 0.8728 (tp) cc_final: 0.8322 (mt) REVERT: X 259 TRP cc_start: 0.7341 (OUTLIER) cc_final: 0.7137 (p90) REVERT: X 286 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7801 (pt) REVERT: X 341 LEU cc_start: 0.7871 (mt) cc_final: 0.6414 (tt) REVERT: H 85 GLU cc_start: 0.6671 (tp30) cc_final: 0.6432 (tp30) REVERT: H 162 VAL cc_start: 0.8721 (t) cc_final: 0.8517 (p) REVERT: L 146 ARG cc_start: 0.8033 (tmt-80) cc_final: 0.7736 (tpt170) outliers start: 45 outliers final: 33 residues processed: 132 average time/residue: 0.0620 time to fit residues: 11.7998 Evaluate side-chains 126 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 247 GLN Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 322 VAL Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 29 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.151616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124208 restraints weight = 10297.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124175 restraints weight = 9527.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124225 restraints weight = 8893.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124300 restraints weight = 8551.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124469 restraints weight = 8454.345| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7349 Z= 0.143 Angle : 0.640 16.231 10023 Z= 0.301 Chirality : 0.040 0.143 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.841 73.143 1039 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.32 % Allowed : 19.09 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.29), residues: 903 helix: 2.76 (0.28), residues: 329 sheet: 1.02 (0.33), residues: 249 loop : -1.14 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 146 TYR 0.011 0.001 TYR L 92 PHE 0.014 0.001 PHE H 91 TRP 0.015 0.001 TRP X 206 HIS 0.009 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7343) covalent geometry : angle 0.63920 (10011) SS BOND : bond 0.00408 ( 6) SS BOND : angle 1.08451 ( 12) hydrogen bonds : bond 0.03571 ( 423) hydrogen bonds : angle 4.28919 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: B 195 GLN cc_start: 0.7874 (pm20) cc_final: 0.7640 (pm20) REVERT: X 79 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5360 (mp10) REVERT: X 205 LEU cc_start: 0.8702 (tp) cc_final: 0.8341 (mt) REVERT: X 259 TRP cc_start: 0.7278 (OUTLIER) cc_final: 0.7044 (p90) REVERT: X 286 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7878 (pt) REVERT: X 341 LEU cc_start: 0.7886 (mt) cc_final: 0.6387 (tt) REVERT: H 20 THR cc_start: 0.8765 (m) cc_final: 0.8528 (p) REVERT: H 85 GLU cc_start: 0.6550 (tp30) cc_final: 0.6347 (tp30) REVERT: L 146 ARG cc_start: 0.8007 (tmt-80) cc_final: 0.7691 (tpt170) outliers start: 41 outliers final: 33 residues processed: 132 average time/residue: 0.0740 time to fit residues: 13.6878 Evaluate side-chains 128 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 247 GLN Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.150315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122866 restraints weight = 10389.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122942 restraints weight = 9210.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122938 restraints weight = 9224.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122987 restraints weight = 8625.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123015 restraints weight = 8489.012| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7349 Z= 0.182 Angle : 0.682 16.797 10023 Z= 0.321 Chirality : 0.041 0.142 1139 Planarity : 0.004 0.042 1240 Dihedral : 6.917 70.303 1039 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.58 % Allowed : 19.22 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.29), residues: 903 helix: 2.56 (0.28), residues: 336 sheet: 0.90 (0.33), residues: 249 loop : -1.09 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 372 TYR 0.013 0.001 TYR L 92 PHE 0.016 0.001 PHE H 91 TRP 0.028 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 7343) covalent geometry : angle 0.68145 (10011) SS BOND : bond 0.00501 ( 6) SS BOND : angle 1.22500 ( 12) hydrogen bonds : bond 0.03781 ( 423) hydrogen bonds : angle 4.38144 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8582 (p0) cc_final: 0.8104 (p0) REVERT: B 195 GLN cc_start: 0.7978 (pm20) cc_final: 0.7670 (pm20) REVERT: X 79 GLN cc_start: 0.6151 (OUTLIER) cc_final: 0.5357 (mp10) REVERT: X 205 LEU cc_start: 0.8734 (tp) cc_final: 0.8319 (mt) REVERT: X 259 TRP cc_start: 0.7351 (OUTLIER) cc_final: 0.7100 (p90) REVERT: X 341 LEU cc_start: 0.7951 (mt) cc_final: 0.6379 (tt) REVERT: H 85 GLU cc_start: 0.6740 (tp30) cc_final: 0.6536 (tp30) REVERT: L 146 ARG cc_start: 0.8048 (tmt-80) cc_final: 0.7735 (tpt170) outliers start: 43 outliers final: 37 residues processed: 129 average time/residue: 0.0683 time to fit residues: 12.7873 Evaluate side-chains 129 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 169 GLU Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 10 optimal weight: 0.0050 chunk 31 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125346 restraints weight = 10215.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125715 restraints weight = 9312.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125979 restraints weight = 8514.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126192 restraints weight = 8005.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126230 restraints weight = 7835.581| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7349 Z= 0.121 Angle : 0.644 16.775 10023 Z= 0.301 Chirality : 0.039 0.142 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.658 65.799 1039 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.68 % Allowed : 20.26 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.29), residues: 903 helix: 2.73 (0.28), residues: 336 sheet: 1.03 (0.33), residues: 249 loop : -0.97 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 372 TYR 0.011 0.001 TYR X 162 PHE 0.012 0.001 PHE L 143 TRP 0.040 0.001 TRP L 152 HIS 0.008 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7343) covalent geometry : angle 0.64388 (10011) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.81149 ( 12) hydrogen bonds : bond 0.03339 ( 423) hydrogen bonds : angle 4.14721 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8385 (p0) cc_final: 0.7943 (p0) REVERT: B 195 GLN cc_start: 0.7926 (pm20) cc_final: 0.7607 (pm20) REVERT: X 79 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5344 (mp10) REVERT: X 205 LEU cc_start: 0.8704 (tp) cc_final: 0.8307 (mt) REVERT: X 259 TRP cc_start: 0.7080 (OUTLIER) cc_final: 0.6860 (p90) REVERT: X 286 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7850 (pt) REVERT: X 341 LEU cc_start: 0.7849 (mt) cc_final: 0.6326 (tt) REVERT: H 20 THR cc_start: 0.8759 (m) cc_final: 0.8496 (p) REVERT: H 85 GLU cc_start: 0.6749 (tp30) cc_final: 0.6545 (tp30) REVERT: H 192 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7653 (p) REVERT: L 146 ARG cc_start: 0.7902 (tmt-80) cc_final: 0.7575 (tpt170) outliers start: 36 outliers final: 29 residues processed: 127 average time/residue: 0.0666 time to fit residues: 12.3014 Evaluate side-chains 130 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain X residue 376 HIS Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 169 GLU Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 232 HIS ** X 247 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 = 0.3804 r_free = 0.3804 target = 0.151442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123395 restraints weight = 10353.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124011 restraints weight = 9453.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124383 restraints weight = 8430.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124454 restraints weight = 7927.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124540 restraints weight = 7980.154| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7349 Z= 0.151 Angle : 0.663 17.167 10023 Z= 0.313 Chirality : 0.040 0.141 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.703 61.683 1039 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.55 % Allowed : 20.78 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.29), residues: 903 helix: 2.65 (0.27), residues: 336 sheet: 1.02 (0.33), residues: 249 loop : -1.01 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 372 TYR 0.011 0.001 TYR L 92 PHE 0.015 0.001 PHE H 91 TRP 0.043 0.001 TRP L 152 HIS 0.008 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7343) covalent geometry : angle 0.66269 (10011) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.11237 ( 12) hydrogen bonds : bond 0.03505 ( 423) hydrogen bonds : angle 4.22994 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 113 SER cc_start: 0.8235 (t) cc_final: 0.7896 (m) REVERT: B 117 ASN cc_start: 0.8449 (p0) cc_final: 0.7994 (p0) REVERT: B 195 GLN cc_start: 0.7952 (pm20) cc_final: 0.7643 (pm20) REVERT: X 79 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5352 (mp10) REVERT: X 117 GLU cc_start: 0.7743 (mp0) cc_final: 0.7212 (mt-10) REVERT: X 205 LEU cc_start: 0.8729 (tp) cc_final: 0.8329 (mt) REVERT: X 259 TRP cc_start: 0.7124 (OUTLIER) cc_final: 0.6904 (p90) REVERT: X 286 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7691 (pt) REVERT: X 341 LEU cc_start: 0.7922 (mt) cc_final: 0.6372 (tt) REVERT: H 20 THR cc_start: 0.8792 (m) cc_final: 0.8512 (p) REVERT: H 192 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7685 (p) REVERT: L 146 ARG cc_start: 0.7964 (tmt-80) cc_final: 0.7662 (tpt170) outliers start: 35 outliers final: 29 residues processed: 121 average time/residue: 0.0576 time to fit residues: 10.1677 Evaluate side-chains 127 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain X residue 376 HIS Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 169 GLU Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 247 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 = 0.3809 r_free = 0.3809 target = 0.151911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124696 restraints weight = 10273.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125083 restraints weight = 9420.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125408 restraints weight = 8435.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125403 restraints weight = 8077.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125437 restraints weight = 7912.722| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7349 Z= 0.158 Angle : 0.663 13.120 10023 Z= 0.315 Chirality : 0.040 0.141 1139 Planarity : 0.004 0.042 1240 Dihedral : 6.671 58.095 1039 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.81 % Allowed : 20.65 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.29), residues: 903 helix: 2.63 (0.27), residues: 336 sheet: 1.03 (0.34), residues: 249 loop : -1.02 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 372 TYR 0.011 0.001 TYR L 92 PHE 0.014 0.001 PHE H 91 TRP 0.046 0.001 TRP L 152 HIS 0.007 0.001 HIS X 376 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7343) covalent geometry : angle 0.66189 (10011) SS BOND : bond 0.00426 ( 6) SS BOND : angle 1.08280 ( 12) hydrogen bonds : bond 0.03572 ( 423) hydrogen bonds : angle 4.28415 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1236.61 seconds wall clock time: 22 minutes 10.37 seconds (1330.37 seconds total)