Starting phenix.real_space_refine on Wed Mar 12 03:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xej_38291/03_2025/8xej_38291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xej_38291/03_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_38291/03_2025/8xej_38291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xej_38291/03_2025/8xej_38291.map" model { file = "/net/cci-nas-00/data/ceres_data/8xej_38291/03_2025/8xej_38291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xej_38291/03_2025/8xej_38291.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.72, per 1000 atoms: 0.66 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: 1.90 Conformation dependent library (CDL) restraints added in 993.9 milliseconds 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: 0.79 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: 2.11 Time building geometry restraints manager: 2.11 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: 0.890 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.600 ------------------------------------------------------------------------------- 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 7343 Z= 0.273 Angle : 0.839 10.874 10011 Z= 0.472 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP X 206 HIS 0.006 0.002 HIS B 205 PHE 0.013 0.002 PHE L 120 TYR 0.017 0.002 TYR L 92 ARG 0.002 0.000 ARG L 62 *********************** 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 : 0.820 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: 0.8831 (mmmm) REVERT: H 111 SER cc_start: 0.7985 (t) cc_final: 0.7748 (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: 0.2201 time to fit residues: 68.4926 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 : 0.797 ------------------------------------------------------------------------------- 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 75 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127301 restraints weight = 10197.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128029 restraints weight = 9049.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128535 restraints weight = 7757.184| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7343 Z= 0.289 Angle : 0.701 12.170 10011 Z= 0.346 Chirality : 0.043 0.208 1139 Planarity : 0.004 0.045 1240 Dihedral : 7.901 91.213 1048 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.03 % Allowed : 16.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.29), residues: 903 helix: 2.76 (0.28), residues: 328 sheet: 0.53 (0.33), residues: 242 loop : -1.51 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 347 HIS 0.006 0.001 HIS B 170 PHE 0.015 0.002 PHE B 159 TYR 0.018 0.002 TYR L 144 ARG 0.003 0.000 ARG H 37 *********************** 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 157 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 79 GLN cc_start: 0.6282 (OUTLIER) cc_final: 0.5562 (mp10) REVERT: X 194 LEU cc_start: 0.4919 (tp) cc_final: 0.4483 (mp) REVERT: X 205 LEU cc_start: 0.8755 (tp) cc_final: 0.8291 (mt) REVERT: X 250 ASP cc_start: 0.8126 (m-30) cc_final: 0.7736 (m-30) REVERT: X 259 TRP cc_start: 0.7269 (OUTLIER) cc_final: 0.7051 (p90) REVERT: X 286 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8074 (pt) REVERT: X 341 LEU cc_start: 0.8060 (mt) cc_final: 0.6759 (tt) REVERT: H 150 THR cc_start: 0.8479 (t) cc_final: 0.8231 (p) REVERT: L 128 GLN cc_start: 0.7387 (tt0) cc_final: 0.7135 (tt0) REVERT: L 169 GLU cc_start: 0.7280 (mp0) cc_final: 0.7006 (mp0) outliers start: 31 outliers final: 19 residues processed: 151 average time/residue: 0.2007 time to fit residues: 40.4849 Evaluate side-chains 116 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 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 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 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 200 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 379 GLN ** L 170 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 = 0.3850 r_free = 0.3850 target = 0.155873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130662 restraints weight = 10277.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129087 restraints weight = 13071.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128576 restraints weight = 10300.062| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7343 Z= 0.219 Angle : 0.644 13.822 10011 Z= 0.314 Chirality : 0.041 0.145 1139 Planarity : 0.004 0.047 1240 Dihedral : 7.376 88.618 1041 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.55 % Allowed : 16.88 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.28), residues: 903 helix: 2.80 (0.28), residues: 328 sheet: 0.84 (0.32), residues: 244 loop : -1.34 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 206 HIS 0.004 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.010 0.001 TYR L 177 ARG 0.002 0.000 ARG X 183 *********************** 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 140 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: X 79 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5552 (mp10) REVERT: X 160 GLU cc_start: 0.7024 (mp0) cc_final: 0.6795 (mp0) REVERT: X 194 LEU cc_start: 0.4781 (tp) cc_final: 0.4419 (mp) REVERT: X 205 LEU cc_start: 0.8734 (tp) cc_final: 0.8286 (mt) REVERT: X 286 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8066 (pt) REVERT: X 341 LEU cc_start: 0.8090 (mt) cc_final: 0.6706 (tt) REVERT: L 128 GLN cc_start: 0.7377 (tt0) cc_final: 0.7159 (tt0) REVERT: L 169 GLU cc_start: 0.7349 (mp0) cc_final: 0.7114 (mp0) outliers start: 35 outliers final: 25 residues processed: 134 average time/residue: 0.1990 time to fit residues: 36.1632 Evaluate side-chains 125 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 63 optimal weight: 0.0170 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 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 = 0.3845 r_free = 0.3845 target = 0.155681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127670 restraints weight = 10252.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128383 restraints weight = 9347.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128818 restraints weight = 8143.624| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7343 Z= 0.172 Angle : 0.630 16.057 10011 Z= 0.297 Chirality : 0.040 0.145 1139 Planarity : 0.004 0.045 1240 Dihedral : 7.124 83.681 1041 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.45 % Allowed : 16.10 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.28), residues: 903 helix: 2.75 (0.28), residues: 330 sheet: 1.06 (0.32), residues: 246 loop : -1.07 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 206 HIS 0.006 0.001 HIS X 376 PHE 0.010 0.001 PHE H 91 TYR 0.015 0.001 TYR L 98 ARG 0.002 0.000 ARG X 183 *********************** 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 152 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: B 129 GLU cc_start: 0.6819 (pm20) cc_final: 0.6511 (mp0) REVERT: X 79 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5603 (mp10) REVERT: X 194 LEU cc_start: 0.4733 (tp) cc_final: 0.4518 (mp) REVERT: X 205 LEU cc_start: 0.8706 (tp) cc_final: 0.8257 (mt) REVERT: X 259 TRP cc_start: 0.7297 (OUTLIER) cc_final: 0.7088 (p90) REVERT: X 286 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8064 (pt) REVERT: X 341 LEU cc_start: 0.7966 (mt) cc_final: 0.6536 (tt) REVERT: X 380 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8839 (mtpp) REVERT: H 20 THR cc_start: 0.8785 (m) cc_final: 0.8542 (p) REVERT: H 162 VAL cc_start: 0.8565 (t) cc_final: 0.8267 (p) REVERT: L 3 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8804 (p) REVERT: L 128 GLN cc_start: 0.7160 (tt0) cc_final: 0.6935 (tt0) REVERT: L 146 ARG cc_start: 0.7801 (tmt-80) cc_final: 0.7211 (tpt170) REVERT: L 169 GLU cc_start: 0.7239 (mp0) cc_final: 0.7008 (mp0) outliers start: 42 outliers final: 28 residues processed: 142 average time/residue: 0.1699 time to fit residues: 33.3644 Evaluate side-chains 132 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 53 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 259 TRP 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 3 VAL 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 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 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 0.0270 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.154448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126690 restraints weight = 10273.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126643 restraints weight = 9106.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126544 restraints weight = 8535.716| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7343 Z= 0.194 Angle : 0.623 15.471 10011 Z= 0.298 Chirality : 0.040 0.145 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.912 79.333 1039 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.94 % Allowed : 16.49 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 903 helix: 2.83 (0.28), residues: 329 sheet: 1.06 (0.32), residues: 249 loop : -1.02 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 206 HIS 0.008 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.014 0.001 TYR L 98 ARG 0.002 0.000 ARG L 146 *********************** 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 144 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: X 79 GLN cc_start: 0.6171 (OUTLIER) cc_final: 0.5423 (mp10) REVERT: X 205 LEU cc_start: 0.8672 (tp) cc_final: 0.8261 (mt) REVERT: X 225 PHE cc_start: 0.7640 (m-80) cc_final: 0.7372 (m-80) REVERT: X 259 TRP cc_start: 0.7338 (OUTLIER) cc_final: 0.7126 (p90) REVERT: X 286 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8088 (pt) REVERT: X 341 LEU cc_start: 0.7760 (mt) cc_final: 0.6497 (tt) REVERT: X 380 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8820 (mtpp) REVERT: H 20 THR cc_start: 0.8795 (m) cc_final: 0.8555 (p) REVERT: H 162 VAL cc_start: 0.8610 (t) cc_final: 0.8332 (p) REVERT: L 146 ARG cc_start: 0.7947 (tmt-80) cc_final: 0.7490 (tpt170) REVERT: L 169 GLU cc_start: 0.7293 (mp0) cc_final: 0.7075 (mp0) outliers start: 38 outliers final: 28 residues processed: 134 average time/residue: 0.1797 time to fit residues: 32.8660 Evaluate side-chains 128 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 B residue 215 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 249 THR Chi-restraints excluded: chain X residue 259 TRP 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 79 optimal weight: 0.0980 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.156218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128748 restraints weight = 10423.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129059 restraints weight = 9331.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129298 restraints weight = 8222.523| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7343 Z= 0.148 Angle : 0.598 15.775 10011 Z= 0.284 Chirality : 0.039 0.143 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.727 76.785 1039 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.25 % Allowed : 18.83 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.29), residues: 903 helix: 2.86 (0.28), residues: 329 sheet: 1.19 (0.33), residues: 249 loop : -0.89 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 206 HIS 0.008 0.001 HIS X 376 PHE 0.008 0.001 PHE H 91 TYR 0.010 0.001 TYR X 162 ARG 0.001 0.000 ARG X 42 *********************** 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 131 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: X 79 GLN cc_start: 0.6087 (OUTLIER) cc_final: 0.5353 (mp10) REVERT: X 205 LEU cc_start: 0.8698 (tp) cc_final: 0.8293 (mt) REVERT: X 259 TRP cc_start: 0.7266 (OUTLIER) cc_final: 0.7060 (p90) REVERT: X 341 LEU cc_start: 0.7757 (mt) cc_final: 0.6473 (tt) REVERT: X 380 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8828 (mtpp) REVERT: H 162 VAL cc_start: 0.8590 (t) cc_final: 0.8307 (p) REVERT: L 128 GLN cc_start: 0.7345 (tt0) cc_final: 0.7134 (tm-30) REVERT: L 146 ARG cc_start: 0.7927 (tmt-80) cc_final: 0.7332 (tpt170) REVERT: L 169 GLU cc_start: 0.7242 (mp0) cc_final: 0.7029 (mp0) outliers start: 25 outliers final: 19 residues processed: 127 average time/residue: 0.1643 time to fit residues: 29.2048 Evaluate side-chains 119 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain X residue 53 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 338 TYR 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 H residue 210 VAL 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 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.155338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128196 restraints weight = 10282.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128156 restraints weight = 9455.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128288 restraints weight = 8929.375| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7343 Z= 0.160 Angle : 0.615 16.433 10011 Z= 0.288 Chirality : 0.039 0.143 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.600 73.885 1039 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.90 % Allowed : 19.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.29), residues: 903 helix: 2.81 (0.28), residues: 329 sheet: 1.28 (0.33), residues: 249 loop : -0.77 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.010 0.001 PHE H 91 TYR 0.017 0.001 TYR X 37 ARG 0.002 0.000 ARG X 284 *********************** 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 131 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.881 Fit side-chains REVERT: X 79 GLN cc_start: 0.6133 (OUTLIER) cc_final: 0.5319 (mp10) REVERT: X 117 GLU cc_start: 0.8069 (mp0) cc_final: 0.7419 (mt-10) REVERT: X 205 LEU cc_start: 0.8724 (tp) cc_final: 0.8313 (mt) REVERT: X 259 TRP cc_start: 0.7278 (OUTLIER) cc_final: 0.7062 (p90) REVERT: X 341 LEU cc_start: 0.7973 (mt) cc_final: 0.6467 (tt) REVERT: X 380 LYS cc_start: 0.8993 (mtpp) cc_final: 0.8638 (mtmm) REVERT: H 162 VAL cc_start: 0.8637 (t) cc_final: 0.8389 (p) REVERT: L 146 ARG cc_start: 0.7916 (tmt-80) cc_final: 0.7430 (tpt170) REVERT: L 169 GLU cc_start: 0.7365 (mp0) cc_final: 0.7160 (mp0) outliers start: 30 outliers final: 24 residues processed: 124 average time/residue: 0.1623 time to fit residues: 28.5324 Evaluate side-chains 126 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 53 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 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 192 THR Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR 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 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.154145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126506 restraints weight = 10294.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126824 restraints weight = 9182.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127145 restraints weight = 8285.179| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7343 Z= 0.185 Angle : 0.633 15.493 10011 Z= 0.296 Chirality : 0.039 0.142 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.591 70.892 1039 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.29 % Allowed : 19.09 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.29), residues: 903 helix: 2.79 (0.28), residues: 330 sheet: 1.32 (0.33), residues: 249 loop : -0.78 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.010 0.001 TYR X 37 ARG 0.002 0.000 ARG X 42 *********************** 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 128 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 1.003 Fit side-chains REVERT: X 79 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5320 (mp10) REVERT: X 205 LEU cc_start: 0.8685 (tp) cc_final: 0.8274 (mt) REVERT: X 259 TRP cc_start: 0.7312 (OUTLIER) cc_final: 0.7090 (p90) REVERT: X 341 LEU cc_start: 0.7979 (mt) cc_final: 0.6451 (tt) REVERT: X 380 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8566 (mtmm) REVERT: H 162 VAL cc_start: 0.8668 (t) cc_final: 0.8423 (p) REVERT: L 169 GLU cc_start: 0.7463 (mp0) cc_final: 0.7238 (mp0) outliers start: 33 outliers final: 29 residues processed: 122 average time/residue: 0.1607 time to fit residues: 28.0358 Evaluate side-chains 124 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 53 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 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 109 THR 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 34 LEU 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 167 VAL 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 25 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 28 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 155 GLN L 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122233 restraints weight = 10310.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122851 restraints weight = 9512.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123097 restraints weight = 8435.079| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7343 Z= 0.289 Angle : 0.685 17.219 10011 Z= 0.327 Chirality : 0.041 0.142 1139 Planarity : 0.004 0.042 1240 Dihedral : 6.808 66.305 1039 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.55 % Allowed : 19.22 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.29), residues: 903 helix: 2.70 (0.28), residues: 330 sheet: 1.20 (0.33), residues: 249 loop : -0.89 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.017 0.001 PHE H 91 TYR 0.014 0.002 TYR L 177 ARG 0.004 0.000 ARG L 146 *********************** 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 134 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.772 Fit side-chains REVERT: X 39 LEU cc_start: 0.7220 (pp) cc_final: 0.6822 (mm) REVERT: X 79 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5231 (mp10) REVERT: X 205 LEU cc_start: 0.8723 (tp) cc_final: 0.8321 (mt) REVERT: X 259 TRP cc_start: 0.7349 (OUTLIER) cc_final: 0.7131 (p90) REVERT: X 341 LEU cc_start: 0.7923 (mt) cc_final: 0.6393 (tt) outliers start: 35 outliers final: 29 residues processed: 128 average time/residue: 0.1609 time to fit residues: 29.2540 Evaluate side-chains 124 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 53 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 320 LEU 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 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 167 VAL 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 40 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.152333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124739 restraints weight = 10415.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125217 restraints weight = 9333.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125349 restraints weight = 8506.351| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7343 Z= 0.215 Angle : 0.655 16.631 10011 Z= 0.310 Chirality : 0.040 0.142 1139 Planarity : 0.004 0.042 1240 Dihedral : 6.655 60.891 1039 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.29 % Allowed : 20.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.29), residues: 903 helix: 2.76 (0.28), residues: 330 sheet: 1.20 (0.34), residues: 249 loop : -0.83 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.014 0.001 PHE H 91 TYR 0.011 0.001 TYR L 92 ARG 0.007 0.000 ARG X 372 ********************** 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 130 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.754 Fit side-chains REVERT: X 39 LEU cc_start: 0.7224 (pp) cc_final: 0.6833 (mm) REVERT: X 79 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.5307 (mp10) REVERT: X 117 GLU cc_start: 0.7924 (mp0) cc_final: 0.7294 (mt-10) REVERT: X 160 GLU cc_start: 0.6695 (mp0) cc_final: 0.6137 (mp0) REVERT: X 205 LEU cc_start: 0.8706 (tp) cc_final: 0.8316 (mt) REVERT: X 259 TRP cc_start: 0.7105 (OUTLIER) cc_final: 0.6903 (p90) REVERT: X 341 LEU cc_start: 0.7900 (mt) cc_final: 0.6373 (tt) outliers start: 33 outliers final: 30 residues processed: 125 average time/residue: 0.1521 time to fit residues: 27.0721 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 : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 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 320 LEU 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 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 167 VAL 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 28 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121007 restraints weight = 10313.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120758 restraints weight = 9851.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120857 restraints weight = 9328.392| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7343 Z= 0.373 Angle : 0.728 16.945 10011 Z= 0.353 Chirality : 0.043 0.142 1139 Planarity : 0.005 0.041 1240 Dihedral : 6.924 58.924 1039 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.16 % Allowed : 20.39 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 903 helix: 2.50 (0.28), residues: 337 sheet: 1.05 (0.34), residues: 249 loop : -0.92 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP L 152 HIS 0.009 0.002 HIS X 376 PHE 0.019 0.002 PHE H 91 TYR 0.018 0.002 TYR L 50 ARG 0.007 0.001 ARG X 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.31 seconds wall clock time: 43 minutes 48.72 seconds (2628.72 seconds total)