Starting phenix.real_space_refine on Fri Jul 19 08:49:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/07_2024/8xej_38291.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/07_2024/8xej_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/07_2024/8xej_38291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/07_2024/8xej_38291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/07_2024/8xej_38291.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/07_2024/8xej_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 Residue "X PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.73, 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 - 3.50 Amino acid : False - 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: 2.89 Conformation dependent library (CDL) restraints added in 1.2 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: 0.78 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: 2.60 Time building geometry restraints manager: 3.11 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: 99.72 - 106.59: 252 106.59 - 113.46: 4048 113.46 - 120.33: 2582 120.33 - 127.20: 3016 127.20 - 134.07: 113 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 2.440 nonbonded pdb=" O MET B 151 " pdb=" OG SER B 154 " model vdw 2.282 2.440 nonbonded pdb=" O ARG X 183 " pdb=" OG1 THR X 187 " model vdw 2.286 2.440 nonbonded pdb=" NH1 ARG X 134 " pdb=" OD2 ASP X 180 " model vdw 2.300 2.520 nonbonded pdb=" NE2 GLN X 105 " pdb=" OD1 ASP X 119 " model vdw 2.336 2.520 ... (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 ========== 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.050 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.820 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 0.723 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: 0.2209 time to fit residues: 68.6800 Evaluate side-chains 129 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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: 0.2980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 247 GLN X 288 HIS X 306 HIS X 317 GLN ** X 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7343 Z= 0.385 Angle : 0.735 12.231 10011 Z= 0.366 Chirality : 0.044 0.203 1139 Planarity : 0.005 0.043 1240 Dihedral : 7.970 93.414 1048 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.55 % Allowed : 16.36 % Favored : 79.09 % 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: 0.82 (0.28), residues: 903 helix: 2.63 (0.28), residues: 328 sheet: 0.41 (0.33), residues: 239 loop : -1.56 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 206 HIS 0.007 0.002 HIS B 170 PHE 0.021 0.002 PHE B 159 TYR 0.020 0.002 TYR L 98 ARG 0.002 0.000 ARG B 184 *********************** 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 162 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8807 (ttp) cc_final: 0.8489 (ttp) REVERT: X 79 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.5541 (mp10) REVERT: X 90 LEU cc_start: 0.7407 (tp) cc_final: 0.7198 (mt) REVERT: X 132 MET cc_start: 0.7617 (mtm) cc_final: 0.7399 (mtm) REVERT: X 194 LEU cc_start: 0.5225 (tp) cc_final: 0.4607 (mp) REVERT: X 205 LEU cc_start: 0.8660 (tp) cc_final: 0.8224 (mt) REVERT: X 250 ASP cc_start: 0.8528 (m-30) cc_final: 0.8102 (m-30) REVERT: X 286 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7825 (pt) REVERT: X 341 LEU cc_start: 0.8149 (mt) cc_final: 0.6730 (tt) REVERT: H 42 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8799 (mmmm) REVERT: H 106 THR cc_start: 0.9416 (p) cc_final: 0.9127 (p) REVERT: H 109 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7907 (p) REVERT: H 150 THR cc_start: 0.8567 (t) cc_final: 0.8325 (p) REVERT: L 128 GLN cc_start: 0.7631 (tt0) cc_final: 0.7214 (tt0) REVERT: L 194 LYS cc_start: 0.6375 (mtpt) cc_final: 0.6145 (tptt) outliers start: 35 outliers final: 22 residues processed: 154 average time/residue: 0.2135 time to fit residues: 42.8026 Evaluate side-chains 118 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 39 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 322 VAL Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 109 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 133 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 151 GLN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3585 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= 0.248 Angle : 0.651 13.777 10011 Z= 0.317 Chirality : 0.041 0.147 1139 Planarity : 0.004 0.047 1240 Dihedral : 7.521 91.363 1043 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.81 % Allowed : 18.31 % Favored : 76.88 % 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: 1.06 (0.28), residues: 903 helix: 2.78 (0.28), residues: 328 sheet: 0.63 (0.32), residues: 241 loop : -1.46 (0.33), residues: 334 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 0.014 0.002 PHE H 91 TYR 0.013 0.002 TYR L 98 ARG 0.003 0.000 ARG X 372 *********************** 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 146 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8771 (ttp) cc_final: 0.8492 (ttp) REVERT: B 129 GLU cc_start: 0.7184 (pm20) cc_final: 0.6828 (mp0) REVERT: B 195 GLN cc_start: 0.8105 (pm20) cc_final: 0.7642 (pm20) REVERT: B 210 TRP cc_start: 0.7397 (t-100) cc_final: 0.7157 (t-100) REVERT: X 79 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.5532 (mp10) REVERT: X 132 MET cc_start: 0.7461 (mtm) cc_final: 0.7157 (mtm) REVERT: X 160 GLU cc_start: 0.7717 (mp0) cc_final: 0.7341 (mp0) REVERT: X 194 LEU cc_start: 0.5000 (tp) cc_final: 0.4474 (mp) REVERT: X 205 LEU cc_start: 0.8630 (tp) cc_final: 0.8178 (mt) REVERT: X 250 ASP cc_start: 0.8452 (m-30) cc_final: 0.8217 (m-30) REVERT: X 259 TRP cc_start: 0.7343 (OUTLIER) cc_final: 0.7089 (p90) REVERT: X 286 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7830 (pt) REVERT: X 341 LEU cc_start: 0.8086 (mt) cc_final: 0.6581 (tt) REVERT: H 85 GLU cc_start: 0.6926 (tp30) cc_final: 0.6632 (tp30) REVERT: H 106 THR cc_start: 0.9421 (p) cc_final: 0.9151 (p) REVERT: L 37 TYR cc_start: 0.8994 (m-80) cc_final: 0.8717 (m-10) REVERT: L 128 GLN cc_start: 0.7504 (tt0) cc_final: 0.7178 (tt0) outliers start: 37 outliers final: 26 residues processed: 139 average time/residue: 0.1600 time to fit residues: 30.8232 Evaluate side-chains 128 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 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 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 73 THR 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 60 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7343 Z= 0.208 Angle : 0.646 17.802 10011 Z= 0.304 Chirality : 0.040 0.187 1139 Planarity : 0.004 0.044 1240 Dihedral : 7.220 88.288 1041 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.06 % Allowed : 18.44 % Favored : 76.49 % 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: 2.69 (0.28), residues: 331 sheet: 0.83 (0.32), residues: 244 loop : -1.24 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 206 HIS 0.006 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.011 0.001 TYR L 92 ARG 0.003 0.000 ARG X 69 *********************** 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 141 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 102 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: B 129 GLU cc_start: 0.7082 (pm20) cc_final: 0.6814 (mp0) REVERT: B 195 GLN cc_start: 0.8079 (pm20) cc_final: 0.7633 (pm20) REVERT: X 79 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5520 (mp10) REVERT: X 132 MET cc_start: 0.7398 (mtm) cc_final: 0.7094 (mtm) REVERT: X 160 GLU cc_start: 0.7617 (mp0) cc_final: 0.7083 (mp0) REVERT: X 194 LEU cc_start: 0.5077 (tp) cc_final: 0.4614 (mp) REVERT: X 205 LEU cc_start: 0.8640 (tp) cc_final: 0.8220 (mt) REVERT: X 225 PHE cc_start: 0.7569 (m-80) cc_final: 0.7335 (m-80) REVERT: X 259 TRP cc_start: 0.7332 (OUTLIER) cc_final: 0.7029 (p90) REVERT: X 341 LEU cc_start: 0.8042 (mt) cc_final: 0.6495 (tt) REVERT: H 106 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9230 (p) REVERT: H 162 VAL cc_start: 0.8715 (t) cc_final: 0.8468 (p) REVERT: L 25 GLN cc_start: 0.8709 (tt0) cc_final: 0.7972 (tt0) REVERT: L 121 ILE cc_start: 0.8624 (tt) cc_final: 0.8374 (mm) outliers start: 39 outliers final: 26 residues processed: 132 average time/residue: 0.1530 time to fit residues: 28.4729 Evaluate side-chains 124 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 318 LEU 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 106 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 169 GLU 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 1 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7343 Z= 0.211 Angle : 0.629 16.904 10011 Z= 0.298 Chirality : 0.040 0.143 1139 Planarity : 0.004 0.044 1240 Dihedral : 7.015 85.472 1039 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.58 % Allowed : 18.31 % Favored : 76.10 % 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: 1.33 (0.29), residues: 903 helix: 2.72 (0.28), residues: 330 sheet: 0.92 (0.33), residues: 244 loop : -1.13 (0.34), residues: 329 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 0.011 0.001 TYR L 92 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 143 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 100 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 129 GLU cc_start: 0.7071 (pm20) cc_final: 0.6864 (mp0) REVERT: B 195 GLN cc_start: 0.8068 (pm20) cc_final: 0.7607 (pm20) REVERT: X 79 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.5423 (mp10) REVERT: X 160 GLU cc_start: 0.7524 (mp0) cc_final: 0.6909 (mp0) REVERT: X 194 LEU cc_start: 0.4786 (tp) cc_final: 0.4500 (mp) REVERT: X 205 LEU cc_start: 0.8588 (tp) cc_final: 0.8142 (mt) REVERT: X 259 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.7080 (p90) REVERT: X 341 LEU cc_start: 0.8028 (mt) cc_final: 0.6473 (tt) REVERT: H 85 GLU cc_start: 0.6995 (tp30) cc_final: 0.6755 (tp30) REVERT: H 162 VAL cc_start: 0.8719 (t) cc_final: 0.8481 (p) REVERT: L 25 GLN cc_start: 0.8722 (tt0) cc_final: 0.8202 (tt0) REVERT: L 121 ILE cc_start: 0.8669 (tt) cc_final: 0.8434 (mm) outliers start: 43 outliers final: 31 residues processed: 134 average time/residue: 0.1506 time to fit residues: 28.7779 Evaluate side-chains 126 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU 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 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 2 ASP Chi-restraints excluded: chain L residue 19 THR 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 169 GLU Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.0980 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7343 Z= 0.167 Angle : 0.603 15.863 10011 Z= 0.283 Chirality : 0.039 0.141 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.746 80.602 1039 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.55 % Allowed : 20.65 % Favored : 74.81 % 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: 1.49 (0.29), residues: 903 helix: 2.81 (0.28), residues: 330 sheet: 0.99 (0.33), residues: 244 loop : -0.99 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 206 HIS 0.004 0.001 HIS X 182 PHE 0.012 0.001 PHE L 143 TYR 0.010 0.001 TYR L 92 ARG 0.004 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 139 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7719 (p0) REVERT: B 129 GLU cc_start: 0.7004 (pm20) cc_final: 0.6780 (mp0) REVERT: X 79 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5192 (mp10) REVERT: X 194 LEU cc_start: 0.4804 (tp) cc_final: 0.4581 (mp) REVERT: X 205 LEU cc_start: 0.8620 (tp) cc_final: 0.8204 (mt) REVERT: X 259 TRP cc_start: 0.7289 (OUTLIER) cc_final: 0.6991 (p90) REVERT: X 341 LEU cc_start: 0.8010 (mt) cc_final: 0.6428 (tt) REVERT: H 20 THR cc_start: 0.8775 (m) cc_final: 0.8453 (p) REVERT: H 85 GLU cc_start: 0.6951 (tp30) cc_final: 0.6675 (tp30) REVERT: H 162 VAL cc_start: 0.8747 (t) cc_final: 0.8545 (p) REVERT: L 25 GLN cc_start: 0.8740 (tt0) cc_final: 0.8060 (tt0) REVERT: L 121 ILE cc_start: 0.8670 (tt) cc_final: 0.8467 (mm) outliers start: 35 outliers final: 26 residues processed: 132 average time/residue: 0.1702 time to fit residues: 31.0088 Evaluate side-chains 127 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 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 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 2 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7343 Z= 0.153 Angle : 0.606 16.509 10011 Z= 0.281 Chirality : 0.039 0.140 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.585 77.500 1039 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.03 % Allowed : 21.69 % Favored : 74.29 % 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: 1.59 (0.29), residues: 903 helix: 2.89 (0.28), residues: 330 sheet: 1.08 (0.33), residues: 244 loop : -0.96 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 206 HIS 0.004 0.001 HIS X 182 PHE 0.011 0.001 PHE L 143 TYR 0.009 0.001 TYR X 162 ARG 0.002 0.000 ARG X 42 *********************** 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 130 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.789 Fit side-chains REVERT: B 117 ASN cc_start: 0.8244 (p0) cc_final: 0.7702 (p0) REVERT: X 79 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5293 (mp10) REVERT: X 129 ASP cc_start: 0.6362 (m-30) cc_final: 0.5964 (m-30) REVERT: X 225 PHE cc_start: 0.7487 (m-80) cc_final: 0.7199 (m-80) REVERT: X 259 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.6962 (p90) REVERT: X 341 LEU cc_start: 0.7983 (mt) cc_final: 0.6411 (tt) REVERT: H 20 THR cc_start: 0.8758 (m) cc_final: 0.8453 (p) REVERT: H 85 GLU cc_start: 0.6895 (tp30) cc_final: 0.6629 (tp30) REVERT: H 162 VAL cc_start: 0.8733 (t) cc_final: 0.8524 (p) REVERT: L 25 GLN cc_start: 0.8666 (tt0) cc_final: 0.8168 (tt0) REVERT: L 121 ILE cc_start: 0.8654 (tt) cc_final: 0.8452 (mm) outliers start: 31 outliers final: 26 residues processed: 124 average time/residue: 0.1651 time to fit residues: 28.6406 Evaluate side-chains 122 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU 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 141 VAL Chi-restraints excluded: chain H residue 150 THR 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 2 ASP Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 8.9990 chunk 54 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4548 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= 0.207 Angle : 0.638 16.802 10011 Z= 0.295 Chirality : 0.039 0.141 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.601 74.874 1039 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.42 % Allowed : 21.69 % Favored : 73.90 % 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: 1.53 (0.29), residues: 903 helix: 2.84 (0.28), residues: 330 sheet: 0.99 (0.33), residues: 249 loop : -0.96 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 152 HIS 0.004 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.011 0.001 TYR L 92 ARG 0.003 0.000 ARG L 146 *********************** 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 125 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 91 time to evaluate : 0.810 Fit side-chains REVERT: B 117 ASN cc_start: 0.8358 (p0) cc_final: 0.7781 (p0) REVERT: X 79 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5293 (mp10) REVERT: X 129 ASP cc_start: 0.6282 (m-30) cc_final: 0.5927 (m-30) REVERT: X 160 GLU cc_start: 0.7658 (mp0) cc_final: 0.7436 (mp0) REVERT: X 259 TRP cc_start: 0.7300 (OUTLIER) cc_final: 0.7013 (p90) REVERT: X 341 LEU cc_start: 0.7988 (mt) cc_final: 0.6396 (tt) REVERT: H 20 THR cc_start: 0.8782 (m) cc_final: 0.8430 (p) REVERT: H 85 GLU cc_start: 0.6950 (tp30) cc_final: 0.6686 (tp30) REVERT: L 25 GLN cc_start: 0.8694 (tt0) cc_final: 0.8220 (tt0) REVERT: L 98 TYR cc_start: 0.8536 (m-10) cc_final: 0.8231 (m-10) REVERT: L 146 ARG cc_start: 0.8246 (tmt-80) cc_final: 0.7885 (tpt170) outliers start: 34 outliers final: 30 residues processed: 118 average time/residue: 0.1586 time to fit residues: 26.5259 Evaluate side-chains 119 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 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 141 VAL Chi-restraints excluded: chain H residue 150 THR 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 2 ASP Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 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 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7343 Z= 0.168 Angle : 0.623 17.410 10011 Z= 0.288 Chirality : 0.039 0.140 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.453 63.455 1039 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.42 % Allowed : 21.56 % Favored : 74.03 % 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: 1.63 (0.29), residues: 903 helix: 2.90 (0.28), residues: 330 sheet: 1.11 (0.33), residues: 249 loop : -0.95 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 152 HIS 0.004 0.001 HIS X 376 PHE 0.011 0.001 PHE L 143 TYR 0.010 0.001 TYR X 162 ARG 0.002 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 123 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 0.784 Fit side-chains REVERT: B 117 ASN cc_start: 0.8354 (p0) cc_final: 0.7814 (p0) REVERT: X 79 GLN cc_start: 0.6059 (OUTLIER) cc_final: 0.5261 (mp10) REVERT: X 129 ASP cc_start: 0.6250 (m-30) cc_final: 0.5891 (m-30) REVERT: X 160 GLU cc_start: 0.7386 (mp0) cc_final: 0.6945 (mp0) REVERT: X 259 TRP cc_start: 0.7100 (OUTLIER) cc_final: 0.6817 (p90) REVERT: X 341 LEU cc_start: 0.7801 (mt) cc_final: 0.6390 (tt) REVERT: H 20 THR cc_start: 0.8737 (m) cc_final: 0.8412 (p) REVERT: H 85 GLU cc_start: 0.6914 (tp30) cc_final: 0.6657 (tp30) REVERT: L 25 GLN cc_start: 0.8675 (tt0) cc_final: 0.8237 (tt0) REVERT: L 98 TYR cc_start: 0.8525 (m-10) cc_final: 0.8246 (m-10) REVERT: L 146 ARG cc_start: 0.8140 (tmt-80) cc_final: 0.7858 (tpt170) outliers start: 34 outliers final: 30 residues processed: 118 average time/residue: 0.1516 time to fit residues: 25.7537 Evaluate side-chains 117 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 85 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 259 TRP Chi-restraints excluded: chain X residue 278 GLU 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 141 VAL Chi-restraints excluded: chain H residue 150 THR 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 2 ASP Chi-restraints excluded: chain L residue 19 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7343 Z= 0.216 Angle : 0.638 15.773 10011 Z= 0.299 Chirality : 0.040 0.172 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.525 59.219 1039 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.29 % Allowed : 22.08 % Favored : 73.64 % 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: 1.57 (0.29), residues: 903 helix: 2.74 (0.27), residues: 337 sheet: 1.14 (0.34), residues: 246 loop : -0.98 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 152 HIS 0.005 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG B 184 ********************** 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 125 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 0.843 Fit side-chains REVERT: B 113 SER cc_start: 0.8379 (t) cc_final: 0.8050 (m) REVERT: B 117 ASN cc_start: 0.8399 (p0) cc_final: 0.7842 (p0) REVERT: X 79 GLN cc_start: 0.6076 (OUTLIER) cc_final: 0.5287 (mp10) REVERT: X 129 ASP cc_start: 0.6147 (m-30) cc_final: 0.5767 (m-30) REVERT: X 259 TRP cc_start: 0.7175 (OUTLIER) cc_final: 0.6892 (p90) REVERT: X 341 LEU cc_start: 0.7985 (mt) cc_final: 0.6369 (tt) REVERT: H 20 THR cc_start: 0.8792 (m) cc_final: 0.8409 (p) REVERT: H 85 GLU cc_start: 0.6943 (tp30) cc_final: 0.6678 (tp30) REVERT: L 25 GLN cc_start: 0.8698 (tt0) cc_final: 0.8012 (tt0) REVERT: L 98 TYR cc_start: 0.8554 (m-10) cc_final: 0.8332 (m-10) REVERT: L 146 ARG cc_start: 0.8192 (tmt-80) cc_final: 0.7930 (tpt170) outliers start: 33 outliers final: 30 residues processed: 119 average time/residue: 0.1674 time to fit residues: 27.9888 Evaluate side-chains 120 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 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 141 VAL Chi-restraints excluded: chain H residue 150 THR 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 2 ASP Chi-restraints excluded: chain L residue 19 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.151386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124216 restraints weight = 10185.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124292 restraints weight = 9016.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124294 restraints weight = 8849.878| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7343 Z= 0.196 Angle : 0.645 15.564 10011 Z= 0.300 Chirality : 0.040 0.170 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.485 57.186 1039 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.42 % Allowed : 22.47 % Favored : 73.12 % 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: 1.55 (0.29), residues: 903 helix: 2.69 (0.28), residues: 337 sheet: 1.09 (0.34), residues: 249 loop : -0.92 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP L 152 HIS 0.006 0.001 HIS X 376 PHE 0.012 0.001 PHE H 91 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG X 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1655.54 seconds wall clock time: 30 minutes 28.21 seconds (1828.21 seconds total)