Starting phenix.real_space_refine on Sat Apr 6 05:28:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/04_2024/8xej_38291_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/04_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_38291/04_2024/8xej_38291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/04_2024/8xej_38291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/04_2024/8xej_38291_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xej_38291/04_2024/8xej_38291_updated.pdb" } 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-5288/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: 4.55, per 1000 atoms: 0.64 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 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... running ksdssp... Secondary structure from input PDB file: 24 helices and 10 sheets defined 36.6% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 210 through 229 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 40 Processing helix chain 'X' and resid 43 through 70 Processing helix chain 'X' and resid 82 through 90 removed outlier: 3.787A pdb=" N LEU X 87 " --> pdb=" O ARG X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 111 Processing helix chain 'X' and resid 117 through 156 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 161 through 187 Processing helix chain 'X' and resid 196 through 224 Proline residue: X 213 - end of helix Processing helix chain 'X' and resid 229 through 246 Processing helix chain 'X' and resid 256 through 271 removed outlier: 3.683A pdb=" N TRP X 259 " --> pdb=" O SER X 256 " (cutoff:3.500A) Processing helix chain 'X' and resid 284 through 305 Processing helix chain 'X' and resid 316 through 339 Proline residue: X 321 - end of helix Processing helix chain 'X' and resid 372 through 381 Processing helix chain 'H' and resid 60 through 62 No H-bonds generated for 'chain 'H' and resid 60 through 62' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 185 through 187 No H-bonds generated for 'chain 'H' and resid 185 through 187' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 95 through 98 No H-bonds generated for 'chain 'L' and resid 95 through 98' Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 187 through 192 Processing sheet with id= A, first strand: chain 'B' and resid 107 through 109 Processing sheet with id= B, first strand: chain 'B' and resid 113 through 117 removed outlier: 8.320A pdb=" N GLU B 114 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR B 199 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE B 116 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ARG B 201 " --> pdb=" O ILE B 116 " (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= C, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= D, first strand: chain 'H' and resid 106 through 108 removed outlier: 3.799A pdb=" N ALA H 32 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG H 37 " --> pdb=" O TRP H 46 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP H 46 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 119 through 123 Processing sheet with id= F, first strand: chain 'H' and resid 150 through 153 Processing sheet with id= G, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= H, first strand: chain 'L' and resid 11 through 15 removed outlier: 6.320A pdb=" N GLU L 107 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA L 14 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL L 109 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA L 85 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 118 through 122 Processing sheet with id= J, first strand: chain 'L' and resid 148 through 154 removed outlier: 3.624A pdb=" N LYS L 211 " --> pdb=" O CYS L 198 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 2.84 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: 1050 2.76 - 3.29: 6708 3.29 - 3.83: 12104 3.83 - 4.36: 13166 4.36 - 4.90: 23692 Nonbonded interactions: 56720 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 56715 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: 3.900 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.100 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.480 ------------------------------------------------------------------------------- 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= 0.257 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 : 0.784 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: 0.2288 time to fit residues: 70.8969 Evaluate side-chains 129 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 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: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 GLN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 7343 Z= 0.452 Angle : 0.756 11.819 10011 Z= 0.380 Chirality : 0.045 0.187 1139 Planarity : 0.005 0.043 1240 Dihedral : 8.094 95.232 1048 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.94 % Allowed : 17.27 % 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: 0.63 (0.28), residues: 903 helix: 2.46 (0.28), residues: 328 sheet: 0.28 (0.33), residues: 241 loop : -1.63 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 259 HIS 0.007 0.002 HIS B 170 PHE 0.022 0.002 PHE B 159 TYR 0.021 0.003 TYR L 92 ARG 0.003 0.001 ARG X 158 *********************** 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 168 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8819 (ttp) cc_final: 0.8506 (ttp) REVERT: X 79 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5447 (mp10) REVERT: X 90 LEU cc_start: 0.7432 (tp) cc_final: 0.7214 (mt) REVERT: X 132 MET cc_start: 0.7664 (mtm) cc_final: 0.7461 (mtm) REVERT: X 160 GLU cc_start: 0.7376 (mp0) cc_final: 0.7019 (mp0) REVERT: X 194 LEU cc_start: 0.4986 (tp) cc_final: 0.4297 (mp) REVERT: X 205 LEU cc_start: 0.8685 (tp) cc_final: 0.8272 (mt) REVERT: X 250 ASP cc_start: 0.8563 (m-30) cc_final: 0.8299 (m-30) REVERT: X 259 TRP cc_start: 0.7580 (OUTLIER) cc_final: 0.7245 (p90) REVERT: X 286 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7822 (pt) REVERT: X 341 LEU cc_start: 0.8111 (mt) cc_final: 0.6839 (tt) REVERT: H 42 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8812 (mmmm) REVERT: H 150 THR cc_start: 0.8572 (t) cc_final: 0.8351 (p) REVERT: L 128 GLN cc_start: 0.7701 (tt0) cc_final: 0.7208 (tt0) REVERT: L 146 ARG cc_start: 0.8361 (tmt-80) cc_final: 0.8045 (tmt-80) REVERT: L 169 GLU cc_start: 0.7787 (mp0) cc_final: 0.7534 (mp0) outliers start: 38 outliers final: 25 residues processed: 159 average time/residue: 0.2040 time to fit residues: 42.5545 Evaluate side-chains 124 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 B residue 223 VAL 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 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 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 28 LEU Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 180 SER 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 44 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 89 HIS X 379 GLN H 170 GLN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7343 Z= 0.228 Angle : 0.633 12.609 10011 Z= 0.308 Chirality : 0.040 0.141 1139 Planarity : 0.004 0.049 1240 Dihedral : 7.467 91.690 1043 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.42 % Allowed : 19.09 % 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: 1.01 (0.28), residues: 903 helix: 2.64 (0.28), residues: 331 sheet: 0.52 (0.32), residues: 243 loop : -1.35 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 206 HIS 0.003 0.001 HIS B 170 PHE 0.013 0.001 PHE H 91 TYR 0.014 0.001 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 143 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 GLU cc_start: 0.7145 (pm20) cc_final: 0.6793 (mp0) REVERT: B 195 GLN cc_start: 0.8082 (pm20) cc_final: 0.7643 (pm20) REVERT: X 79 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.5548 (mp10) REVERT: X 90 LEU cc_start: 0.7410 (tp) cc_final: 0.7156 (mt) REVERT: X 132 MET cc_start: 0.7423 (mtm) cc_final: 0.7115 (mtm) REVERT: X 160 GLU cc_start: 0.7603 (mp0) cc_final: 0.7333 (mp0) REVERT: X 194 LEU cc_start: 0.4923 (tp) cc_final: 0.4099 (mp) REVERT: X 205 LEU cc_start: 0.8709 (tp) cc_final: 0.8241 (mt) REVERT: X 259 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.7258 (p90) REVERT: X 286 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7817 (pt) REVERT: X 341 LEU cc_start: 0.8073 (mt) cc_final: 0.6795 (tt) REVERT: H 106 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9236 (p) REVERT: L 169 GLU cc_start: 0.7757 (mp0) cc_final: 0.7538 (mp0) outliers start: 34 outliers final: 22 residues processed: 136 average time/residue: 0.1777 time to fit residues: 33.4595 Evaluate side-chains 123 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 109 THR 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 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 89 HIS X 275 ASN ** L 128 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7343 Z= 0.241 Angle : 0.650 17.670 10011 Z= 0.307 Chirality : 0.040 0.140 1139 Planarity : 0.004 0.046 1240 Dihedral : 7.260 89.072 1041 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.45 % Allowed : 17.92 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.28), residues: 903 helix: 2.55 (0.28), residues: 331 sheet: 0.57 (0.32), residues: 246 loop : -1.15 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 206 HIS 0.005 0.001 HIS X 376 PHE 0.014 0.001 PHE H 91 TYR 0.014 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 143 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 101 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7697 (p0) REVERT: B 129 GLU cc_start: 0.7132 (pm20) cc_final: 0.6861 (mp0) REVERT: B 195 GLN cc_start: 0.8106 (pm20) cc_final: 0.7647 (pm20) REVERT: X 79 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.5550 (mp10) REVERT: X 90 LEU cc_start: 0.7461 (tp) cc_final: 0.7239 (mt) REVERT: X 132 MET cc_start: 0.7494 (mtm) cc_final: 0.7197 (mtm) REVERT: X 194 LEU cc_start: 0.5025 (tp) cc_final: 0.4132 (mp) REVERT: X 205 LEU cc_start: 0.8667 (tp) cc_final: 0.8237 (mt) REVERT: X 259 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.6839 (m100) REVERT: X 286 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7652 (pt) REVERT: X 341 LEU cc_start: 0.8057 (mt) cc_final: 0.6740 (tt) REVERT: H 106 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9155 (p) REVERT: L 25 GLN cc_start: 0.8737 (tt0) cc_final: 0.8245 (tt0) REVERT: L 128 GLN cc_start: 0.7601 (tt0) cc_final: 0.7166 (tt0) REVERT: L 169 GLU cc_start: 0.7763 (mp0) cc_final: 0.7561 (mp0) outliers start: 42 outliers final: 26 residues processed: 134 average time/residue: 0.1863 time to fit residues: 35.0047 Evaluate side-chains 128 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 123 MET Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 320 LEU Chi-restraints excluded: chain X residue 322 VAL Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 109 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 89 HIS X 163 GLN L 28 GLN L 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7343 Z= 0.403 Angle : 0.725 19.606 10011 Z= 0.351 Chirality : 0.042 0.157 1139 Planarity : 0.005 0.042 1240 Dihedral : 7.397 83.677 1037 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 6.49 % Allowed : 18.44 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.28), residues: 903 helix: 2.29 (0.28), residues: 331 sheet: 0.24 (0.32), residues: 247 loop : -1.18 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 206 HIS 0.008 0.002 HIS X 376 PHE 0.019 0.002 PHE H 91 TYR 0.021 0.002 TYR L 50 ARG 0.004 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 144 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 94 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: B 195 GLN cc_start: 0.8235 (pm20) cc_final: 0.7775 (pm20) REVERT: X 79 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.5499 (mp10) REVERT: X 90 LEU cc_start: 0.7711 (tp) cc_final: 0.7403 (mt) REVERT: X 132 MET cc_start: 0.7668 (mtm) cc_final: 0.7398 (mtm) REVERT: X 205 LEU cc_start: 0.8721 (tp) cc_final: 0.8297 (mt) REVERT: X 210 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8124 (mp) REVERT: X 259 TRP cc_start: 0.7461 (OUTLIER) cc_final: 0.7101 (m100) REVERT: X 286 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7478 (pt) REVERT: L 25 GLN cc_start: 0.8768 (tt0) cc_final: 0.8111 (tt0) outliers start: 50 outliers final: 34 residues processed: 134 average time/residue: 0.1614 time to fit residues: 30.8056 Evaluate side-chains 120 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 82 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 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 210 LEU Chi-restraints excluded: chain X residue 231 LEU Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU Chi-restraints excluded: chain X residue 286 ILE Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 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 28 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 109 THR 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 139 LEU 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 50 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 49 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 89 HIS ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4435 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= 0.206 Angle : 0.635 17.465 10011 Z= 0.299 Chirality : 0.039 0.141 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.923 80.615 1037 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.94 % Allowed : 21.82 % Favored : 73.25 % 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: 1.01 (0.28), residues: 903 helix: 2.50 (0.28), residues: 330 sheet: 0.51 (0.32), residues: 249 loop : -1.17 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 206 HIS 0.008 0.001 HIS X 376 PHE 0.013 0.001 PHE L 143 TYR 0.012 0.001 TYR L 92 ARG 0.002 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 133 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 95 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: B 129 GLU cc_start: 0.7281 (pm20) cc_final: 0.6917 (mp0) REVERT: B 195 GLN cc_start: 0.8162 (pm20) cc_final: 0.7687 (pm20) REVERT: X 79 GLN cc_start: 0.6284 (OUTLIER) cc_final: 0.5466 (mp10) REVERT: X 90 LEU cc_start: 0.7703 (tp) cc_final: 0.7397 (mt) REVERT: X 132 MET cc_start: 0.7479 (mtm) cc_final: 0.7166 (mtm) REVERT: X 160 GLU cc_start: 0.7091 (mp0) cc_final: 0.6005 (mp0) REVERT: X 194 LEU cc_start: 0.4536 (tp) cc_final: 0.3314 (mp) REVERT: X 205 LEU cc_start: 0.8698 (tp) cc_final: 0.8275 (mt) REVERT: X 210 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8167 (mp) REVERT: X 259 TRP cc_start: 0.7511 (OUTLIER) cc_final: 0.7145 (m100) REVERT: X 286 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7641 (pt) REVERT: H 85 GLU cc_start: 0.6975 (tp30) cc_final: 0.6738 (tp30) REVERT: H 106 THR cc_start: 0.9424 (OUTLIER) cc_final: 0.9131 (p) REVERT: L 25 GLN cc_start: 0.8745 (tt0) cc_final: 0.8036 (tt0) REVERT: L 121 ILE cc_start: 0.8716 (tt) cc_final: 0.8486 (mm) outliers start: 38 outliers final: 29 residues processed: 127 average time/residue: 0.1600 time to fit residues: 28.9280 Evaluate side-chains 122 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 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 210 LEU Chi-restraints excluded: chain X residue 247 GLN Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 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 23 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 149 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 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 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 85 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 89 HIS X 155 GLN X 163 GLN H 170 GLN L 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4509 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= 0.170 Angle : 0.602 15.220 10011 Z= 0.283 Chirality : 0.039 0.139 1139 Planarity : 0.004 0.045 1240 Dihedral : 6.611 76.977 1037 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.06 % Allowed : 21.95 % Favored : 72.99 % 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: 1.21 (0.29), residues: 903 helix: 2.58 (0.28), residues: 331 sheet: 0.77 (0.32), residues: 244 loop : -1.09 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 206 HIS 0.008 0.001 HIS X 376 PHE 0.013 0.001 PHE L 143 TYR 0.013 0.001 TYR B 229 ARG 0.003 0.000 ARG L 146 *********************** 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 144 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 0.826 Fit side-chains REVERT: B 117 ASN cc_start: 0.8355 (p0) cc_final: 0.7804 (p0) REVERT: B 129 GLU cc_start: 0.7152 (pm20) cc_final: 0.6848 (mp0) REVERT: B 195 GLN cc_start: 0.8100 (pm20) cc_final: 0.7574 (pm20) REVERT: B 229 TYR cc_start: 0.8604 (t80) cc_final: 0.7905 (t80) REVERT: X 79 GLN cc_start: 0.6261 (OUTLIER) cc_final: 0.5455 (mp10) REVERT: X 90 LEU cc_start: 0.7712 (tp) cc_final: 0.7395 (mt) REVERT: X 160 GLU cc_start: 0.7077 (mp0) cc_final: 0.5981 (mp0) REVERT: X 194 LEU cc_start: 0.4569 (tp) cc_final: 0.3357 (mp) REVERT: X 205 LEU cc_start: 0.8610 (tp) cc_final: 0.8208 (mt) REVERT: X 259 TRP cc_start: 0.7420 (OUTLIER) cc_final: 0.7119 (m100) REVERT: H 20 THR cc_start: 0.8800 (m) cc_final: 0.8470 (p) REVERT: H 85 GLU cc_start: 0.6978 (tp30) cc_final: 0.6716 (tp30) REVERT: L 25 GLN cc_start: 0.8713 (tt0) cc_final: 0.8308 (tt0) REVERT: L 121 ILE cc_start: 0.8707 (tt) cc_final: 0.8488 (mm) REVERT: L 128 GLN cc_start: 0.7469 (tt0) cc_final: 0.7094 (tt0) outliers start: 39 outliers final: 30 residues processed: 135 average time/residue: 0.1555 time to fit residues: 29.6847 Evaluate side-chains 128 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 79 GLN Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 247 GLN Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 259 TRP Chi-restraints excluded: chain X residue 278 GLU 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 149 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 6 THR 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 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 16 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4649 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= 0.198 Angle : 0.612 15.959 10011 Z= 0.289 Chirality : 0.039 0.139 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.512 68.173 1037 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.94 % Allowed : 21.82 % Favored : 73.25 % 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: 1.18 (0.29), residues: 903 helix: 2.58 (0.28), residues: 331 sheet: 0.69 (0.32), residues: 249 loop : -1.10 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 152 HIS 0.008 0.001 HIS X 376 PHE 0.013 0.001 PHE L 143 TYR 0.011 0.001 TYR B 229 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 135 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 97 time to evaluate : 0.799 Fit side-chains REVERT: B 117 ASN cc_start: 0.8324 (p0) cc_final: 0.7723 (p0) REVERT: B 129 GLU cc_start: 0.7130 (pm20) cc_final: 0.6845 (mp0) REVERT: B 195 GLN cc_start: 0.8107 (pm20) cc_final: 0.7569 (pm20) REVERT: X 79 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5305 (mp10) REVERT: X 90 LEU cc_start: 0.7657 (tp) cc_final: 0.7349 (mt) REVERT: X 160 GLU cc_start: 0.7217 (mp0) cc_final: 0.6267 (mp0) REVERT: X 194 LEU cc_start: 0.4500 (tp) cc_final: 0.3338 (mp) REVERT: X 259 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.7087 (m100) REVERT: H 20 THR cc_start: 0.8804 (m) cc_final: 0.8479 (p) REVERT: H 85 GLU cc_start: 0.7038 (tp30) cc_final: 0.6770 (tp30) REVERT: L 25 GLN cc_start: 0.8698 (tt0) cc_final: 0.7996 (tt0) REVERT: L 128 GLN cc_start: 0.7411 (tt0) cc_final: 0.7138 (tt0) outliers start: 38 outliers final: 34 residues processed: 129 average time/residue: 0.1700 time to fit residues: 30.2874 Evaluate side-chains 126 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 90 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain 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 49 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 149 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 6 THR 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 139 LEU 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: 3.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 163 GLN ** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4772 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= 0.215 Angle : 0.630 16.325 10011 Z= 0.295 Chirality : 0.039 0.139 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.493 62.799 1037 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.06 % Allowed : 21.82 % 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: 1.14 (0.29), residues: 903 helix: 2.39 (0.28), residues: 336 sheet: 0.77 (0.33), residues: 244 loop : -1.07 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.014 0.001 PHE H 91 TYR 0.016 0.001 TYR L 98 ARG 0.002 0.000 ARG X 42 *********************** 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 129 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 0.852 Fit side-chains REVERT: B 117 ASN cc_start: 0.8362 (p0) cc_final: 0.7754 (p0) REVERT: B 129 GLU cc_start: 0.7097 (pm20) cc_final: 0.6815 (mp0) REVERT: B 195 GLN cc_start: 0.8114 (pm20) cc_final: 0.7571 (pm20) REVERT: X 79 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5382 (mp10) REVERT: X 90 LEU cc_start: 0.7671 (tp) cc_final: 0.7371 (mt) REVERT: X 160 GLU cc_start: 0.6988 (mp0) cc_final: 0.6092 (mp0) REVERT: X 194 LEU cc_start: 0.4447 (tp) cc_final: 0.3333 (mp) REVERT: X 259 TRP cc_start: 0.7361 (OUTLIER) cc_final: 0.7032 (m100) REVERT: H 85 GLU cc_start: 0.7069 (tp30) cc_final: 0.6805 (tp30) REVERT: H 192 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7835 (p) REVERT: L 25 GLN cc_start: 0.8713 (tt0) cc_final: 0.8016 (tt0) REVERT: L 128 GLN cc_start: 0.7417 (tt0) cc_final: 0.7147 (tt0) outliers start: 39 outliers final: 33 residues processed: 122 average time/residue: 0.1686 time to fit residues: 29.5497 Evaluate side-chains 125 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 89 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain 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 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 49 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 149 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 6 THR 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 139 LEU 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: 0.7980 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7343 Z= 0.238 Angle : 0.639 17.466 10011 Z= 0.301 Chirality : 0.039 0.140 1139 Planarity : 0.004 0.043 1240 Dihedral : 6.616 57.317 1037 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.94 % Allowed : 21.82 % Favored : 73.25 % 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: 1.05 (0.29), residues: 903 helix: 2.35 (0.28), residues: 335 sheet: 0.68 (0.33), residues: 246 loop : -1.10 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.015 0.001 PHE H 91 TYR 0.015 0.001 TYR L 98 ARG 0.002 0.000 ARG X 42 ********************** 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 131 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 93 time to evaluate : 0.813 Fit side-chains REVERT: B 113 SER cc_start: 0.8411 (t) cc_final: 0.8068 (m) REVERT: B 117 ASN cc_start: 0.8416 (p0) cc_final: 0.7804 (p0) REVERT: B 129 GLU cc_start: 0.7114 (pm20) cc_final: 0.6836 (mp0) REVERT: B 176 MET cc_start: 0.7907 (mmm) cc_final: 0.7632 (tpt) REVERT: B 195 GLN cc_start: 0.8131 (pm20) cc_final: 0.7597 (pm20) REVERT: X 79 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.5397 (mp10) REVERT: X 90 LEU cc_start: 0.7683 (tp) cc_final: 0.7388 (mt) REVERT: X 117 GLU cc_start: 0.8067 (mp0) cc_final: 0.7562 (mt-10) REVERT: X 160 GLU cc_start: 0.6972 (mp0) cc_final: 0.6063 (mp0) REVERT: X 194 LEU cc_start: 0.4499 (tp) cc_final: 0.3395 (mp) REVERT: X 259 TRP cc_start: 0.7172 (OUTLIER) cc_final: 0.6892 (m100) REVERT: H 85 GLU cc_start: 0.7025 (tp30) cc_final: 0.6806 (tp30) REVERT: H 192 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7767 (p) REVERT: L 25 GLN cc_start: 0.8720 (tt0) cc_final: 0.8234 (tt0) outliers start: 38 outliers final: 33 residues processed: 125 average time/residue: 0.1600 time to fit residues: 28.4065 Evaluate side-chains 124 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain 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 49 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 149 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 6 THR 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 139 LEU 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: 3.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 101 GLN ** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123529 restraints weight = 10188.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124177 restraints weight = 9303.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124550 restraints weight = 8047.354| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4962 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= 0.215 Angle : 0.644 16.269 10011 Z= 0.300 Chirality : 0.039 0.139 1139 Planarity : 0.004 0.044 1240 Dihedral : 6.488 59.330 1037 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.94 % Allowed : 21.95 % 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: 1.07 (0.29), residues: 903 helix: 2.37 (0.28), residues: 334 sheet: 0.70 (0.33), residues: 246 loop : -1.10 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP L 152 HIS 0.009 0.001 HIS X 376 PHE 0.013 0.001 PHE H 91 TYR 0.018 0.001 TYR L 98 ARG 0.002 0.000 ARG L 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1703.00 seconds wall clock time: 31 minutes 47.27 seconds (1907.27 seconds total)