Starting phenix.real_space_refine on Wed Mar 12 05:25:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h87_34531/03_2025/8h87_34531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h87_34531/03_2025/8h87_34531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h87_34531/03_2025/8h87_34531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h87_34531/03_2025/8h87_34531.map" model { file = "/net/cci-nas-00/data/ceres_data/8h87_34531/03_2025/8h87_34531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h87_34531/03_2025/8h87_34531.cif" } resolution = 2.53 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= 0.009 sd= 0.430 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 3 5.49 5 S 48 5.16 5 C 4830 2.51 5 N 978 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7083 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2097 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 264 Unusual residues: {'PLM': 9, 'PSC': 6, 'RET': 1} Classifications: {'undetermined': 16, 'water': 49} Link IDs: {None: 64} Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 4, 'PSC:plan-2': 4, 'PSC:plan-3': 4, 'PSC:plan-4': 4, 'PLM:plan-1': 8} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Restraints were copied for chains: C, B Time building chain proxies: 4.49, per 1000 atoms: 0.63 Number of scatterers: 7083 At special positions: 0 Unit cell: (78.02, 77.19, 84.66, 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 48 16.00 P 3 15.00 O 1224 8.00 N 978 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 72.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 414 hydrogen bonds defined for protein. 1233 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: 1.90 Time building geometry restraints manager: 2.03 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: 1169 1.33 - 1.46: 2602 1.46 - 1.59: 3288 1.59 - 1.72: 6 1.72 - 1.85: 63 Bond restraints: 7128 Sorted by residual: bond pdb=" C6 PSC A 404 " pdb=" C7 PSC A 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C6 PSC C 404 " pdb=" C7 PSC C 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C6 PSC B 404 " pdb=" C7 PSC B 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" CA SER A 217 " pdb=" CB SER A 217 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.61e-02 3.86e+03 1.75e+01 bond pdb=" CA SER C 217 " pdb=" CB SER C 217 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.61e-02 3.86e+03 1.72e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 9373 4.08 - 8.16: 101 8.16 - 12.24: 12 12.24 - 16.32: 12 16.32 - 20.41: 3 Bond angle restraints: 9501 Sorted by residual: angle pdb=" C01 PSC B 402 " pdb=" C02 PSC B 402 " pdb=" O01 PSC B 402 " ideal model delta sigma weight residual 107.00 127.41 -20.41 3.00e+00 1.11e-01 4.63e+01 angle pdb=" C01 PSC C 402 " pdb=" C02 PSC C 402 " pdb=" O01 PSC C 402 " ideal model delta sigma weight residual 107.00 127.40 -20.40 3.00e+00 1.11e-01 4.62e+01 angle pdb=" C01 PSC A 402 " pdb=" C02 PSC A 402 " pdb=" O01 PSC A 402 " ideal model delta sigma weight residual 107.00 127.39 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" N PRO C 182 " pdb=" CA PRO C 182 " pdb=" C PRO C 182 " ideal model delta sigma weight residual 113.75 121.44 -7.69 1.49e+00 4.50e-01 2.67e+01 angle pdb=" N PRO A 182 " pdb=" CA PRO A 182 " pdb=" C PRO A 182 " ideal model delta sigma weight residual 113.75 121.44 -7.69 1.49e+00 4.50e-01 2.66e+01 ... (remaining 9496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 3900 32.13 - 64.27: 213 64.27 - 96.40: 12 96.40 - 128.53: 3 128.53 - 160.67: 3 Dihedral angle restraints: 4131 sinusoidal: 1869 harmonic: 2262 Sorted by residual: dihedral pdb=" N PSC A 402 " pdb=" C04 PSC A 402 " pdb=" C05 PSC A 402 " pdb=" O12 PSC A 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.22 -160.67 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N PSC B 402 " pdb=" C04 PSC B 402 " pdb=" C05 PSC B 402 " pdb=" O12 PSC B 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.21 -160.66 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N PSC C 402 " pdb=" C04 PSC C 402 " pdb=" C05 PSC C 402 " pdb=" O12 PSC C 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.20 -160.65 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 4128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 460 0.049 - 0.098: 261 0.098 - 0.147: 139 0.147 - 0.196: 43 0.196 - 0.245: 24 Chirality restraints: 927 Sorted by residual: chirality pdb=" CB VAL B 17 " pdb=" CA VAL B 17 " pdb=" CG1 VAL B 17 " pdb=" CG2 VAL B 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL C 17 " pdb=" CA VAL C 17 " pdb=" CG1 VAL C 17 " pdb=" CG2 VAL C 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL A 17 " pdb=" CA VAL A 17 " pdb=" CG1 VAL A 17 " pdb=" CG2 VAL A 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 924 not shown) Planarity restraints: 1137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 402 " -0.246 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" C11 PSC A 402 " 0.088 2.00e-02 2.50e+03 pdb=" C8 PSC A 402 " -0.089 2.00e-02 2.50e+03 pdb=" C9 PSC A 402 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 402 " 0.246 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" C11 PSC C 402 " -0.088 2.00e-02 2.50e+03 pdb=" C8 PSC C 402 " 0.089 2.00e-02 2.50e+03 pdb=" C9 PSC C 402 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 402 " 0.246 2.00e-02 2.50e+03 1.85e-01 3.42e+02 pdb=" C11 PSC B 402 " -0.088 2.00e-02 2.50e+03 pdb=" C8 PSC B 402 " 0.089 2.00e-02 2.50e+03 pdb=" C9 PSC B 402 " -0.247 2.00e-02 2.50e+03 ... (remaining 1134 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2114 2.82 - 3.34: 6640 3.34 - 3.86: 12755 3.86 - 4.38: 16441 4.38 - 4.90: 25046 Nonbonded interactions: 62996 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" O HOH A 501 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR C 180 " pdb=" O HOH C 501 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 180 " pdb=" O HOH B 501 " model vdw 2.301 3.040 nonbonded pdb=" N GLY A 52 " pdb=" OE1 GLU A 248 " model vdw 2.333 3.120 nonbonded pdb=" N GLY B 52 " pdb=" OE1 GLU B 248 " model vdw 2.333 3.120 ... (remaining 62991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.680 Find NCS groups from input model: 0.140 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:14.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.011 0.209 7128 Z= 0.673 Angle : 1.547 20.406 9501 Z= 0.941 Chirality : 0.080 0.245 927 Planarity : 0.017 0.185 1137 Dihedral : 18.835 160.666 2691 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.91 % Allowed : 1.82 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.27), residues: 771 helix: -1.08 (0.18), residues: 516 sheet: None (None), residues: 0 loop : 0.02 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.011 TRP C 42 HIS 0.012 0.006 HIS C 225 PHE 0.050 0.010 PHE A 150 TYR 0.043 0.010 TYR A 101 ARG 0.018 0.002 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ASP cc_start: 0.8294 (m-30) cc_final: 0.7947 (m-30) REVERT: A 171 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6401 (ttp-170) REVERT: A 174 LYS cc_start: 0.7676 (mtpm) cc_final: 0.7077 (mtmt) REVERT: A 186 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7023 (ttm110) REVERT: A 204 LEU cc_start: 0.7840 (tp) cc_final: 0.7525 (mt) REVERT: A 235 ILE cc_start: 0.7628 (mm) cc_final: 0.7405 (mt) REVERT: B 4 TYR cc_start: 0.8153 (t80) cc_final: 0.7940 (t80) REVERT: B 5 ASP cc_start: 0.8288 (m-30) cc_final: 0.8018 (m-30) REVERT: B 14 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.6862 (mmp-170) REVERT: B 171 ARG cc_start: 0.7391 (ttt-90) cc_final: 0.6602 (ttp-170) REVERT: B 174 LYS cc_start: 0.7774 (mtpm) cc_final: 0.7222 (mtmp) REVERT: B 204 LEU cc_start: 0.7739 (tp) cc_final: 0.7474 (mt) REVERT: C 5 ASP cc_start: 0.8412 (m-30) cc_final: 0.8078 (m-30) REVERT: C 43 MET cc_start: 0.7930 (mtt) cc_final: 0.7695 (mtt) REVERT: C 171 ARG cc_start: 0.7205 (ttt-90) cc_final: 0.6382 (ttp-170) REVERT: C 174 LYS cc_start: 0.7698 (mtpm) cc_final: 0.7172 (mtmp) REVERT: C 186 ARG cc_start: 0.7992 (ttt180) cc_final: 0.6898 (ttm110) REVERT: C 204 LEU cc_start: 0.7704 (tp) cc_final: 0.7489 (mt) REVERT: C 230 LEU cc_start: 0.7623 (tp) cc_final: 0.7392 (tp) outliers start: 6 outliers final: 2 residues processed: 89 average time/residue: 1.4676 time to fit residues: 136.7772 Evaluate side-chains 82 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.136321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130667 restraints weight = 6502.437| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.36 r_work: 0.3306 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 7128 Z= 0.420 Angle : 1.145 18.517 9501 Z= 0.604 Chirality : 0.066 0.699 927 Planarity : 0.014 0.178 1137 Dihedral : 21.972 148.283 1300 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.28 % Favored : 95.33 % Rotamer: Outliers : 2.73 % Allowed : 6.97 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.28), residues: 771 helix: -0.61 (0.20), residues: 519 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.009 TRP C 161 HIS 0.049 0.006 HIS C 215 PHE 0.077 0.007 PHE B 238 TYR 0.099 0.008 TYR B 129 ARG 0.048 0.003 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8243 (ttt-90) cc_final: 0.7731 (ttp-170) REVERT: A 174 LYS cc_start: 0.8808 (mtpm) cc_final: 0.8491 (mtmp) REVERT: A 175 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8277 (mtmt) REVERT: A 186 ARG cc_start: 0.8807 (ttt180) cc_final: 0.8328 (ttm110) REVERT: B 4 TYR cc_start: 0.8985 (t80) cc_final: 0.8780 (t80) REVERT: B 14 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7867 (mmm160) REVERT: B 171 ARG cc_start: 0.8310 (ttt-90) cc_final: 0.7635 (ttp-170) REVERT: B 174 LYS cc_start: 0.8792 (mtpm) cc_final: 0.8483 (mtmp) REVERT: C 171 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7750 (ttp-170) REVERT: C 174 LYS cc_start: 0.8784 (mtpm) cc_final: 0.8411 (mtmp) REVERT: C 182 PRO cc_start: 0.8651 (OUTLIER) cc_final: 0.8450 (Cg_exo) REVERT: C 230 LEU cc_start: 0.8766 (tp) cc_final: 0.8559 (tp) REVERT: C 252 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7907 (mm-30) outliers start: 18 outliers final: 5 residues processed: 94 average time/residue: 1.8947 time to fit residues: 186.2161 Evaluate side-chains 79 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 182 PRO Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 0.0570 chunk 74 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.1600 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.137144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131670 restraints weight = 6554.928| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.35 r_work: 0.3350 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7128 Z= 0.170 Angle : 0.560 7.306 9501 Z= 0.284 Chirality : 0.040 0.127 927 Planarity : 0.005 0.053 1137 Dihedral : 20.806 148.663 1300 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.36 % Allowed : 8.79 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.29), residues: 771 helix: 1.49 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.42 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 42 HIS 0.002 0.001 HIS A 225 PHE 0.017 0.002 PHE B 238 TYR 0.013 0.002 TYR B 103 ARG 0.002 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.997 Fit side-chains REVERT: A 171 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7440 (ttp-170) REVERT: A 174 LYS cc_start: 0.8726 (mtpm) cc_final: 0.8404 (mtmp) REVERT: A 186 ARG cc_start: 0.8712 (ttt180) cc_final: 0.8234 (ttm110) REVERT: B 4 TYR cc_start: 0.8894 (t80) cc_final: 0.8694 (t80) REVERT: B 5 ASP cc_start: 0.8475 (m-30) cc_final: 0.8244 (m-30) REVERT: B 171 ARG cc_start: 0.8134 (ttt-90) cc_final: 0.7561 (ttp-170) REVERT: B 174 LYS cc_start: 0.8802 (mtpm) cc_final: 0.8407 (mtmm) REVERT: C 171 ARG cc_start: 0.8066 (ttt-90) cc_final: 0.7576 (ttp-170) REVERT: C 244 ARG cc_start: 0.8942 (mtt90) cc_final: 0.8562 (mtm110) outliers start: 9 outliers final: 3 residues processed: 89 average time/residue: 1.8699 time to fit residues: 173.7802 Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127794 restraints weight = 6728.705| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.36 r_work: 0.3301 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7128 Z= 0.251 Angle : 0.627 7.929 9501 Z= 0.312 Chirality : 0.043 0.175 927 Planarity : 0.005 0.046 1137 Dihedral : 20.355 147.979 1300 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.73 % Allowed : 8.03 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.29), residues: 771 helix: 1.83 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.61 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 42 HIS 0.004 0.001 HIS A 225 PHE 0.018 0.002 PHE B 208 TYR 0.015 0.002 TYR B 81 ARG 0.003 0.001 ARG C 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.748 Fit side-chains REVERT: A 171 ARG cc_start: 0.8157 (ttt-90) cc_final: 0.7559 (ttp-170) REVERT: A 174 LYS cc_start: 0.8742 (mtpm) cc_final: 0.8397 (mtmp) REVERT: A 186 ARG cc_start: 0.8742 (ttt180) cc_final: 0.8231 (ttm110) REVERT: B 5 ASP cc_start: 0.8597 (m-30) cc_final: 0.8355 (m-30) REVERT: B 171 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7613 (ttp-170) REVERT: B 174 LYS cc_start: 0.8823 (mtpm) cc_final: 0.8443 (mtmm) REVERT: C 171 ARG cc_start: 0.8119 (ttt-90) cc_final: 0.7695 (ttp-170) REVERT: C 252 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7891 (mm-30) outliers start: 18 outliers final: 8 residues processed: 80 average time/residue: 1.7112 time to fit residues: 143.2355 Evaluate side-chains 77 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127526 restraints weight = 6672.892| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.35 r_work: 0.3294 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7128 Z= 0.253 Angle : 0.615 7.942 9501 Z= 0.307 Chirality : 0.042 0.160 927 Planarity : 0.005 0.045 1137 Dihedral : 20.131 146.506 1300 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.03 % Allowed : 6.97 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.29), residues: 771 helix: 1.88 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.62 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 42 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.002 PHE A 134 TYR 0.014 0.002 TYR B 81 ARG 0.003 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.746 Fit side-chains REVERT: A 171 ARG cc_start: 0.8140 (ttt-90) cc_final: 0.7545 (ttp-170) REVERT: A 174 LYS cc_start: 0.8737 (mtpm) cc_final: 0.8392 (mtmp) REVERT: A 186 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8248 (ttm110) REVERT: B 5 ASP cc_start: 0.8669 (m-30) cc_final: 0.8424 (m-30) REVERT: B 171 ARG cc_start: 0.8232 (ttt-90) cc_final: 0.7604 (ttp-170) REVERT: B 174 LYS cc_start: 0.8812 (mtpm) cc_final: 0.8428 (mtmm) REVERT: C 171 ARG cc_start: 0.8116 (ttt-90) cc_final: 0.7698 (ttp-170) REVERT: C 252 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7895 (mm-30) outliers start: 20 outliers final: 8 residues processed: 80 average time/residue: 1.4127 time to fit residues: 118.7196 Evaluate side-chains 79 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 0.0670 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128588 restraints weight = 6660.355| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.34 r_work: 0.3313 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7128 Z= 0.222 Angle : 0.578 7.703 9501 Z= 0.290 Chirality : 0.041 0.141 927 Planarity : 0.005 0.043 1137 Dihedral : 19.510 145.265 1300 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.27 % Allowed : 8.18 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.30 (0.29), residues: 771 helix: 2.00 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.62 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 42 HIS 0.003 0.001 HIS A 225 PHE 0.014 0.002 PHE A 134 TYR 0.012 0.002 TYR B 81 ARG 0.002 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.694 Fit side-chains REVERT: A 171 ARG cc_start: 0.8107 (ttt-90) cc_final: 0.7532 (ttp-170) REVERT: A 174 LYS cc_start: 0.8713 (mtpm) cc_final: 0.8382 (mtmp) REVERT: B 5 ASP cc_start: 0.8614 (m-30) cc_final: 0.8385 (m-30) REVERT: B 171 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7579 (ttp-170) REVERT: B 174 LYS cc_start: 0.8798 (mtpm) cc_final: 0.8415 (mtmm) REVERT: C 171 ARG cc_start: 0.8107 (ttt-90) cc_final: 0.7667 (ttp-170) REVERT: C 252 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7840 (mm-30) outliers start: 15 outliers final: 8 residues processed: 79 average time/residue: 1.4446 time to fit residues: 119.5426 Evaluate side-chains 80 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 0.0170 chunk 7 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 125 GLN C 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122655 restraints weight = 6436.710| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 0.43 r_work: 0.3234 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7128 Z= 0.146 Angle : 0.499 7.042 9501 Z= 0.249 Chirality : 0.038 0.129 927 Planarity : 0.005 0.038 1137 Dihedral : 18.428 141.791 1300 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.36 % Allowed : 9.55 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.72 (0.29), residues: 771 helix: 2.32 (0.21), residues: 528 sheet: None (None), residues: 0 loop : 0.74 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 42 HIS 0.002 0.000 HIS A 225 PHE 0.012 0.001 PHE A 134 TYR 0.008 0.001 TYR A 81 ARG 0.002 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.750 Fit side-chains REVERT: A 171 ARG cc_start: 0.7889 (ttt-90) cc_final: 0.7317 (ttp-170) REVERT: A 174 LYS cc_start: 0.8682 (mtpm) cc_final: 0.8310 (mtmp) REVERT: B 5 ASP cc_start: 0.8443 (m-30) cc_final: 0.8222 (m-30) REVERT: B 171 ARG cc_start: 0.8002 (ttt-90) cc_final: 0.7415 (ttp-170) REVERT: B 174 LYS cc_start: 0.8735 (mtpm) cc_final: 0.8327 (mtmm) REVERT: C 171 ARG cc_start: 0.7931 (ttt-90) cc_final: 0.7480 (ttp-170) outliers start: 9 outliers final: 3 residues processed: 82 average time/residue: 1.5800 time to fit residues: 135.4949 Evaluate side-chains 76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118773 restraints weight = 6565.779| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 0.45 r_work: 0.3134 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7128 Z= 0.224 Angle : 0.576 7.771 9501 Z= 0.288 Chirality : 0.041 0.147 927 Planarity : 0.005 0.039 1137 Dihedral : 18.575 143.257 1300 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.67 % Allowed : 9.39 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.52 (0.29), residues: 771 helix: 2.19 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.66 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 42 HIS 0.004 0.001 HIS A 225 PHE 0.015 0.002 PHE A 134 TYR 0.012 0.002 TYR B 81 ARG 0.002 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.670 Fit side-chains REVERT: A 171 ARG cc_start: 0.8134 (ttt-90) cc_final: 0.7524 (ttp-170) REVERT: A 174 LYS cc_start: 0.8802 (mtpm) cc_final: 0.8424 (mtmp) REVERT: B 5 ASP cc_start: 0.8688 (m-30) cc_final: 0.8455 (m-30) REVERT: B 171 ARG cc_start: 0.8210 (ttt-90) cc_final: 0.7590 (ttp-170) REVERT: B 174 LYS cc_start: 0.8844 (mtpm) cc_final: 0.8438 (mtmm) REVERT: C 76 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 171 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7682 (ttp-170) outliers start: 11 outliers final: 5 residues processed: 78 average time/residue: 1.4136 time to fit residues: 115.7507 Evaluate side-chains 76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.126822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119930 restraints weight = 6580.678| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 0.45 r_work: 0.3155 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7128 Z= 0.185 Angle : 0.542 7.498 9501 Z= 0.270 Chirality : 0.039 0.132 927 Planarity : 0.005 0.038 1137 Dihedral : 18.301 142.337 1300 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.06 % Allowed : 9.55 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.57 (0.29), residues: 771 helix: 2.24 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.65 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 42 HIS 0.003 0.001 HIS C 225 PHE 0.015 0.001 PHE A 134 TYR 0.010 0.002 TYR C 81 ARG 0.002 0.000 ARG C 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.736 Fit side-chains REVERT: A 171 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7726 (ttp80) REVERT: A 174 LYS cc_start: 0.8787 (mtpm) cc_final: 0.8419 (mtmp) REVERT: B 171 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.7550 (ttp-170) REVERT: B 174 LYS cc_start: 0.8832 (mtpm) cc_final: 0.8417 (mtmm) REVERT: C 76 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8552 (mt) REVERT: C 171 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7643 (ttp-170) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 1.4960 time to fit residues: 122.4096 Evaluate side-chains 82 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.129418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122584 restraints weight = 6645.333| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 0.45 r_work: 0.3232 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7128 Z= 0.154 Angle : 0.504 7.127 9501 Z= 0.251 Chirality : 0.038 0.129 927 Planarity : 0.005 0.037 1137 Dihedral : 17.680 140.317 1300 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.91 % Allowed : 9.85 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.75 (0.30), residues: 771 helix: 2.36 (0.21), residues: 528 sheet: None (None), residues: 0 loop : 0.73 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 42 HIS 0.002 0.001 HIS B 225 PHE 0.013 0.001 PHE A 134 TYR 0.009 0.001 TYR A 106 ARG 0.001 0.000 ARG C 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.731 Fit side-chains REVERT: A 171 ARG cc_start: 0.7982 (ttt-90) cc_final: 0.7395 (ttp-170) REVERT: A 174 LYS cc_start: 0.8679 (mtpm) cc_final: 0.8303 (mtmp) REVERT: B 171 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7437 (ttp-170) REVERT: B 174 LYS cc_start: 0.8713 (mtpm) cc_final: 0.8304 (mtmm) REVERT: C 76 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8500 (mt) REVERT: C 171 ARG cc_start: 0.7983 (ttt-90) cc_final: 0.7511 (ttp-170) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 1.4573 time to fit residues: 125.6509 Evaluate side-chains 79 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126337 restraints weight = 6707.154| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 0.36 r_work: 0.3283 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7128 Z= 0.333 Angle : 0.685 8.525 9501 Z= 0.341 Chirality : 0.046 0.223 927 Planarity : 0.005 0.042 1137 Dihedral : 18.724 144.016 1300 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.06 % Allowed : 9.85 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.28), residues: 771 helix: 1.93 (0.20), residues: 522 sheet: None (None), residues: 0 loop : 0.48 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 42 HIS 0.005 0.002 HIS A 225 PHE 0.018 0.002 PHE B 208 TYR 0.017 0.002 TYR B 81 ARG 0.004 0.001 ARG A 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4730.60 seconds wall clock time: 84 minutes 17.55 seconds (5057.55 seconds total)