Starting phenix.real_space_refine on Tue Jan 14 19:13:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xej_38291/01_2025/8xej_38291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xej_38291/01_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_38291/01_2025/8xej_38291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xej_38291/01_2025/8xej_38291.map" model { file = "/net/cci-nas-00/data/ceres_data/8xej_38291/01_2025/8xej_38291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xej_38291/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 4.43, per 1000 atoms: 0.62 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: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.15 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: 2.27 Time building geometry restraints manager: 2.14 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: 1.530 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- 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 : 0.765 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: 0.2295 time to fit residues: 71.2486 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 : 0.752 ------------------------------------------------------------------------------- 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 = 0.156546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127805 restraints weight = 10199.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128485 restraints weight = 8456.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128711 restraints weight = 7648.272| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 12.163 10011 Z= 0.346 Chirality : 0.043 0.208 1139 Planarity : 0.004 0.045 1240 Dihedral : 7.901 91.226 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 : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 79 GLN cc_start: 0.6293 (OUTLIER) cc_final: 0.5560 (mp10) REVERT: X 194 LEU cc_start: 0.4973 (tp) cc_final: 0.4503 (mp) REVERT: X 205 LEU cc_start: 0.8752 (tp) cc_final: 0.8286 (mt) REVERT: X 250 ASP cc_start: 0.8175 (m-30) cc_final: 0.7783 (m-30) REVERT: X 259 TRP cc_start: 0.7276 (OUTLIER) cc_final: 0.7051 (p90) REVERT: X 286 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8051 (pt) REVERT: X 341 LEU cc_start: 0.8079 (mt) cc_final: 0.6761 (tt) REVERT: H 150 THR cc_start: 0.8494 (t) cc_final: 0.8242 (p) REVERT: L 128 GLN cc_start: 0.7393 (tt0) cc_final: 0.7139 (tt0) REVERT: L 169 GLU cc_start: 0.7280 (mp0) cc_final: 0.7025 (mp0) outliers start: 31 outliers final: 19 residues processed: 151 average time/residue: 0.2057 time to fit residues: 41.0553 Evaluate side-chains 117 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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: 0.6980 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.154446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127323 restraints weight = 10302.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127732 restraints weight = 9463.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127893 restraints weight = 8586.353| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7343 Z= 0.248 Angle : 0.664 13.477 10011 Z= 0.323 Chirality : 0.041 0.146 1139 Planarity : 0.004 0.046 1240 Dihedral : 7.504 89.731 1041 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.68 % Allowed : 16.75 % 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: 1.19 (0.28), residues: 903 helix: 2.77 (0.28), residues: 328 sheet: 0.80 (0.32), residues: 244 loop : -1.35 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 206 HIS 0.004 0.001 HIS B 170 PHE 0.014 0.001 PHE H 91 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG L 146 *********************** 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 141 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8758 (ttp) cc_final: 0.8510 (ttp) REVERT: X 79 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5544 (mp10) REVERT: X 194 LEU cc_start: 0.5015 (tp) cc_final: 0.4536 (mp) REVERT: X 205 LEU cc_start: 0.8741 (tp) cc_final: 0.8276 (mt) REVERT: X 286 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8067 (pt) REVERT: X 341 LEU cc_start: 0.8115 (mt) cc_final: 0.6727 (tt) REVERT: H 109 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7755 (p) REVERT: L 128 GLN cc_start: 0.7383 (tt0) cc_final: 0.7129 (tt0) REVERT: L 169 GLU cc_start: 0.7351 (mp0) cc_final: 0.7126 (mp0) outliers start: 36 outliers final: 25 residues processed: 135 average time/residue: 0.2024 time to fit residues: 36.6896 Evaluate side-chains 121 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 H residue 109 THR 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 167 VAL 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: 0.0040 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 151 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 = 0.3849 r_free = 0.3849 target = 0.155807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128591 restraints weight = 10195.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128808 restraints weight = 9087.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129088 restraints weight = 8288.446| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7343 Z= 0.188 Angle : 0.637 17.107 10011 Z= 0.303 Chirality : 0.040 0.148 1139 Planarity : 0.004 0.044 1240 Dihedral : 7.202 84.886 1041 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.45 % Allowed : 15.97 % 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: 1.36 (0.28), residues: 903 helix: 2.70 (0.28), residues: 330 sheet: 0.96 (0.32), residues: 246 loop : -1.10 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 206 HIS 0.007 0.001 HIS X 376 PHE 0.012 0.001 PHE H 91 TYR 0.015 0.001 TYR L 98 ARG 0.002 0.000 ARG L 146 *********************** 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 : 0.808 Fit side-chains revert: symmetry clash REVERT: X 79 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5558 (mp10) REVERT: X 194 LEU cc_start: 0.4683 (tp) cc_final: 0.4432 (mp) REVERT: X 205 LEU cc_start: 0.8725 (tp) cc_final: 0.8304 (mt) REVERT: X 286 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.8022 (pt) REVERT: X 341 LEU cc_start: 0.7928 (mt) cc_final: 0.6518 (tt) REVERT: H 20 THR cc_start: 0.8803 (m) cc_final: 0.8552 (p) REVERT: H 162 VAL cc_start: 0.8571 (t) cc_final: 0.8282 (p) REVERT: L 128 GLN cc_start: 0.7134 (tt0) cc_final: 0.6929 (tt0) REVERT: L 146 ARG cc_start: 0.7802 (tmt-80) cc_final: 0.7264 (tpt170) REVERT: L 169 GLU cc_start: 0.7259 (mp0) cc_final: 0.7034 (mp0) outliers start: 42 outliers final: 27 residues processed: 143 average time/residue: 0.1622 time to fit residues: 32.6227 Evaluate side-chains 125 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 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 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 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 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 113 THR Chi-restraints excluded: chain L residue 133 THR 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: 1.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.151342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122764 restraints weight = 10322.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122713 restraints weight = 9776.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122570 restraints weight = 9349.516| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7343 Z= 0.275 Angle : 0.679 18.155 10011 Z= 0.322 Chirality : 0.041 0.147 1139 Planarity : 0.004 0.043 1240 Dihedral : 7.179 81.343 1039 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.19 % Allowed : 17.01 % Favored : 77.79 % 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: 1.31 (0.29), residues: 903 helix: 2.67 (0.28), residues: 329 sheet: 0.90 (0.32), residues: 249 loop : -1.12 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 206 HIS 0.009 0.001 HIS X 376 PHE 0.016 0.001 PHE H 91 TYR 0.014 0.002 TYR L 98 ARG 0.002 0.000 ARG B 184 *********************** 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: 40 poor density : 99 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: B 129 GLU cc_start: 0.7128 (pm20) cc_final: 0.6796 (mp0) REVERT: X 79 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5464 (mp10) REVERT: X 205 LEU cc_start: 0.8680 (tp) cc_final: 0.8233 (mt) REVERT: X 286 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7943 (pt) REVERT: X 341 LEU cc_start: 0.7932 (mt) cc_final: 0.6487 (tt) REVERT: L 169 GLU cc_start: 0.7361 (mp0) cc_final: 0.7154 (mp0) outliers start: 40 outliers final: 27 residues processed: 131 average time/residue: 0.1659 time to fit residues: 30.4467 Evaluate side-chains 120 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 B residue 215 ILE 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 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 178 SER 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 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: 0.9990 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.153441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125854 restraints weight = 10446.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125854 restraints weight = 10831.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125854 restraints weight = 10831.049| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7343 Z= 0.181 Angle : 0.639 17.221 10011 Z= 0.300 Chirality : 0.040 0.147 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.896 77.530 1039 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.77 % Allowed : 18.83 % 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 (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: 2.79 (0.28), residues: 329 sheet: 1.04 (0.33), residues: 249 loop : -0.96 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 206 HIS 0.010 0.001 HIS X 376 PHE 0.012 0.001 PHE L 143 TYR 0.010 0.001 TYR L 92 ARG 0.003 0.000 ARG L 146 *********************** 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 128 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: X 39 LEU cc_start: 0.7313 (pp) cc_final: 0.7053 (tp) REVERT: X 79 GLN cc_start: 0.5996 (OUTLIER) cc_final: 0.5224 (mp10) REVERT: X 205 LEU cc_start: 0.8655 (tp) cc_final: 0.8212 (mt) REVERT: X 286 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7939 (pt) REVERT: X 341 LEU cc_start: 0.7776 (mt) cc_final: 0.6476 (tt) REVERT: H 20 THR cc_start: 0.8803 (m) cc_final: 0.8558 (p) REVERT: H 162 VAL cc_start: 0.8582 (t) cc_final: 0.8345 (p) REVERT: L 146 ARG cc_start: 0.8047 (tmt-80) cc_final: 0.7547 (tpt170) REVERT: L 169 GLU cc_start: 0.7461 (mp0) cc_final: 0.7257 (mp0) outliers start: 29 outliers final: 23 residues processed: 123 average time/residue: 0.1845 time to fit residues: 31.4909 Evaluate side-chains 116 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 286 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 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 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 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: 2.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.151619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123575 restraints weight = 10388.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123868 restraints weight = 9527.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123977 restraints weight = 8575.215| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7343 Z= 0.215 Angle : 0.642 16.469 10011 Z= 0.302 Chirality : 0.040 0.144 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.814 74.667 1039 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.19 % Allowed : 17.40 % 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 (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: 2.77 (0.28), residues: 329 sheet: 1.08 (0.33), residues: 249 loop : -0.96 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 206 HIS 0.010 0.001 HIS X 376 PHE 0.014 0.001 PHE H 91 TYR 0.011 0.001 TYR L 92 ARG 0.008 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 135 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: X 79 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.5286 (mp10) REVERT: X 160 GLU cc_start: 0.6989 (mp0) cc_final: 0.6721 (mp0) REVERT: X 205 LEU cc_start: 0.8672 (tp) cc_final: 0.8252 (mt) REVERT: X 259 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.7101 (p90) REVERT: X 286 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7888 (pt) REVERT: X 341 LEU cc_start: 0.7836 (mt) cc_final: 0.6392 (tt) REVERT: H 20 THR cc_start: 0.8796 (m) cc_final: 0.8561 (p) REVERT: H 162 VAL cc_start: 0.8640 (t) cc_final: 0.8397 (p) REVERT: L 146 ARG cc_start: 0.7988 (tmt-80) cc_final: 0.7672 (tpt170) outliers start: 40 outliers final: 32 residues processed: 128 average time/residue: 0.1728 time to fit residues: 31.3445 Evaluate side-chains 126 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 231 LEU 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 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 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 6 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 0.1980 chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** X 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123692 restraints weight = 10516.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124261 restraints weight = 9833.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124491 restraints weight = 8491.015| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7343 Z= 0.180 Angle : 0.645 16.669 10011 Z= 0.301 Chirality : 0.040 0.141 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.665 71.367 1039 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.55 % Allowed : 19.09 % Favored : 76.36 % 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: 1.60 (0.29), residues: 903 helix: 2.75 (0.28), residues: 330 sheet: 1.17 (0.33), residues: 249 loop : -0.89 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 206 HIS 0.009 0.001 HIS X 376 PHE 0.011 0.001 PHE H 91 TYR 0.009 0.001 TYR X 162 ARG 0.006 0.000 ARG X 372 *********************** 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 133 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: X 79 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.5363 (mp10) REVERT: X 117 GLU cc_start: 0.7741 (mp0) cc_final: 0.7183 (mt-10) REVERT: X 160 GLU cc_start: 0.6976 (mp0) cc_final: 0.6692 (mp0) REVERT: X 205 LEU cc_start: 0.8665 (tp) cc_final: 0.8242 (mt) REVERT: X 259 TRP cc_start: 0.7291 (OUTLIER) cc_final: 0.7047 (p90) REVERT: X 286 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7864 (pt) REVERT: X 341 LEU cc_start: 0.7747 (mt) cc_final: 0.6404 (tt) REVERT: H 20 THR cc_start: 0.8738 (m) cc_final: 0.8504 (p) REVERT: H 162 VAL cc_start: 0.8677 (t) cc_final: 0.8467 (p) REVERT: L 146 ARG cc_start: 0.8007 (tmt-80) cc_final: 0.7512 (tpt170) outliers start: 35 outliers final: 29 residues processed: 126 average time/residue: 0.1646 time to fit residues: 29.2697 Evaluate side-chains 125 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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 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 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 6 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 53 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 155 GLN ** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.122020 restraints weight = 10313.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122227 restraints weight = 8901.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122299 restraints weight = 8499.042| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7343 Z= 0.301 Angle : 0.694 17.116 10011 Z= 0.328 Chirality : 0.041 0.141 1139 Planarity : 0.004 0.042 1240 Dihedral : 6.857 67.345 1039 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.68 % Allowed : 19.61 % Favored : 75.71 % 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: 1.44 (0.29), residues: 903 helix: 2.65 (0.28), residues: 330 sheet: 1.04 (0.33), residues: 249 loop : -0.96 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.016 0.002 PHE H 91 TYR 0.015 0.002 TYR L 50 ARG 0.006 0.000 ARG X 372 *********************** 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 130 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 1.022 Fit side-chains REVERT: X 79 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5392 (mp10) REVERT: X 117 GLU cc_start: 0.7824 (mp0) cc_final: 0.7269 (mt-10) REVERT: X 160 GLU cc_start: 0.7066 (mp0) cc_final: 0.6748 (mp0) REVERT: X 205 LEU cc_start: 0.8735 (tp) cc_final: 0.8309 (mt) REVERT: X 259 TRP cc_start: 0.7351 (OUTLIER) cc_final: 0.7117 (p90) REVERT: X 286 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7664 (pt) REVERT: X 341 LEU cc_start: 0.7864 (mt) cc_final: 0.6352 (tt) outliers start: 36 outliers final: 31 residues processed: 123 average time/residue: 0.1603 time to fit residues: 28.2877 Evaluate side-chains 125 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 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 286 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3806 r_free = 0.3806 target = 0.151638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123976 restraints weight = 10431.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124416 restraints weight = 9026.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124564 restraints weight = 8249.584| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7343 Z= 0.211 Angle : 0.673 17.214 10011 Z= 0.316 Chirality : 0.040 0.141 1139 Planarity : 0.004 0.042 1240 Dihedral : 6.708 62.665 1039 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.55 % Allowed : 20.00 % 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: 1.45 (0.29), residues: 903 helix: 2.51 (0.28), residues: 337 sheet: 1.06 (0.33), residues: 249 loop : -0.88 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.011 0.001 TYR L 92 ARG 0.006 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: 35 poor density : 95 time to evaluate : 0.768 Fit side-chains REVERT: X 79 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5243 (mp10) REVERT: X 117 GLU cc_start: 0.7747 (mp0) cc_final: 0.7214 (mt-10) REVERT: X 129 ASP cc_start: 0.6736 (m-30) cc_final: 0.6428 (m-30) REVERT: X 160 GLU cc_start: 0.6957 (mp0) cc_final: 0.6651 (mp0) REVERT: X 205 LEU cc_start: 0.8695 (tp) cc_final: 0.8261 (mt) REVERT: X 259 TRP cc_start: 0.7125 (OUTLIER) cc_final: 0.6864 (p90) REVERT: X 286 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7744 (pt) REVERT: X 341 LEU cc_start: 0.7852 (mt) cc_final: 0.6297 (tt) REVERT: H 20 THR cc_start: 0.8776 (m) cc_final: 0.8539 (p) REVERT: H 192 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7589 (p) outliers start: 35 outliers final: 29 residues processed: 122 average time/residue: 0.1585 time to fit residues: 27.6349 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 : 0.891 ------------------------------------------------------------------------------- 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 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 286 ILE 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 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 53 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 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 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.0770 chunk 15 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.151842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124502 restraints weight = 10244.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124900 restraints weight = 8685.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125097 restraints weight = 8073.410| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4869 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= 0.211 Angle : 0.671 17.363 10011 Z= 0.314 Chirality : 0.040 0.179 1139 Planarity : 0.004 0.042 1240 Dihedral : 6.644 59.561 1039 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.81 % Allowed : 20.00 % 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 (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: 2.56 (0.27), residues: 337 sheet: 1.09 (0.34), residues: 249 loop : -0.83 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.011 0.001 TYR L 92 ARG 0.006 0.000 ARG X 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2305.60 seconds wall clock time: 43 minutes 4.16 seconds (2584.16 seconds total)