Starting phenix.real_space_refine on Fri Jul 25 08:32:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h87_34531/07_2025/8h87_34531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h87_34531/07_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_34531/07_2025/8h87_34531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h87_34531/07_2025/8h87_34531.map" model { file = "/net/cci-nas-00/data/ceres_data/8h87_34531/07_2025/8h87_34531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h87_34531/07_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-5711/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: 5.03, per 1000 atoms: 0.71 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: 2.15 Conformation dependent library (CDL) restraints added in 2.5 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: 0.51 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: 2.21 Time building geometry restraints manager: 2.54 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: 0.04 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: 58.490 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.140 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:204.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 286.660 ------------------------------------------------------------------------------- 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 7131 Z= 0.729 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 Details of bonding type rmsd hydrogen bonds : bond 0.17238 ( 414) hydrogen bonds : angle 7.56513 ( 1233) covalent geometry : bond 0.01079 ( 7128) covalent geometry : angle 1.54697 ( 9501) Misc. bond : bond 0.16257 ( 3) *********************** 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 : 0.816 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: 2.8637 time to fit residues: 267.5647 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 : 2.100 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.135525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129776 restraints weight = 6497.544| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 0.37 r_work: 0.3285 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 7131 Z= 0.295 Angle : 1.160 18.064 9501 Z= 0.617 Chirality : 0.066 0.515 927 Planarity : 0.014 0.160 1137 Dihedral : 21.940 146.757 1300 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.41 % Favored : 95.33 % Rotamer: Outliers : 2.42 % Allowed : 7.12 % Favored : 90.45 % 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: -0.84 (0.28), residues: 771 helix: -0.48 (0.20), residues: 519 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.009 TRP C 161 HIS 0.045 0.006 HIS C 215 PHE 0.076 0.007 PHE B 238 TYR 0.097 0.008 TYR B 129 ARG 0.047 0.004 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.09324 ( 414) hydrogen bonds : angle 5.77113 ( 1233) covalent geometry : bond 0.00632 ( 7128) covalent geometry : angle 1.15994 ( 9501) Misc. bond : bond 0.00376 ( 3) *********************** 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 102 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8266 (ttt-90) cc_final: 0.7767 (ttp-170) REVERT: A 174 LYS cc_start: 0.8796 (mtpm) cc_final: 0.8480 (mtmp) REVERT: A 175 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8153 (mtmt) REVERT: A 186 ARG cc_start: 0.8797 (ttt180) cc_final: 0.8337 (ttm110) REVERT: B 4 TYR cc_start: 0.9009 (t80) cc_final: 0.8806 (t80) REVERT: B 171 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.7670 (ttp-170) REVERT: B 174 LYS cc_start: 0.8802 (mtpm) cc_final: 0.8452 (mtmp) REVERT: C 43 MET cc_start: 0.8842 (mtt) cc_final: 0.8553 (mtt) REVERT: C 171 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7727 (ttp-170) REVERT: C 174 LYS cc_start: 0.8782 (mtpm) cc_final: 0.8452 (mtmp) REVERT: C 182 PRO cc_start: 0.8642 (OUTLIER) cc_final: 0.8409 (Cg_exo) REVERT: C 230 LEU cc_start: 0.8810 (tp) cc_final: 0.8600 (tp) outliers start: 16 outliers final: 4 residues processed: 95 average time/residue: 1.4723 time to fit residues: 146.7806 Evaluate side-chains 77 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.136549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130969 restraints weight = 6541.072| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 0.35 r_work: 0.3340 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7131 Z= 0.134 Angle : 0.568 7.267 9501 Z= 0.289 Chirality : 0.040 0.127 927 Planarity : 0.005 0.054 1137 Dihedral : 20.950 148.623 1300 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.52 % Allowed : 8.79 % Favored : 89.70 % 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: 1.70 (0.29), residues: 771 helix: 1.55 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.39 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 42 HIS 0.002 0.001 HIS B 225 PHE 0.017 0.002 PHE B 238 TYR 0.013 0.002 TYR B 103 ARG 0.003 0.000 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.05319 ( 414) hydrogen bonds : angle 4.36052 ( 1233) covalent geometry : bond 0.00285 ( 7128) covalent geometry : angle 0.56767 ( 9501) Misc. bond : bond 0.00059 ( 3) *********************** 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 92 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.742 Fit side-chains REVERT: A 171 ARG cc_start: 0.8088 (ttt-90) cc_final: 0.7504 (ttp-170) REVERT: A 174 LYS cc_start: 0.8724 (mtpm) cc_final: 0.8402 (mtmp) REVERT: A 186 ARG cc_start: 0.8700 (ttt180) cc_final: 0.8233 (ttm110) REVERT: B 5 ASP cc_start: 0.8509 (m-30) cc_final: 0.8301 (m-30) REVERT: B 171 ARG cc_start: 0.8153 (ttt-90) cc_final: 0.7915 (ttp-110) REVERT: B 174 LYS cc_start: 0.8801 (mtpm) cc_final: 0.8416 (mtmm) REVERT: C 171 ARG cc_start: 0.8075 (ttt-90) cc_final: 0.7599 (ttp-170) REVERT: C 174 LYS cc_start: 0.8723 (mtpm) cc_final: 0.8393 (mtmp) REVERT: C 244 ARG cc_start: 0.8953 (mtt90) cc_final: 0.8703 (mtm110) REVERT: C 252 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7896 (mm-30) outliers start: 10 outliers final: 3 residues processed: 87 average time/residue: 1.6479 time to fit residues: 149.7021 Evaluate side-chains 70 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 252 GLU 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: 20.0000 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.135340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129593 restraints weight = 6657.811| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.38 r_work: 0.3306 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7131 Z= 0.163 Angle : 0.610 7.911 9501 Z= 0.304 Chirality : 0.042 0.157 927 Planarity : 0.005 0.046 1137 Dihedral : 20.337 147.913 1300 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.18 % Allowed : 7.42 % 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: 2.19 (0.29), residues: 771 helix: 1.94 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.56 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 42 HIS 0.004 0.001 HIS A 225 PHE 0.016 0.002 PHE C 208 TYR 0.015 0.002 TYR B 81 ARG 0.003 0.000 ARG C 218 Details of bonding type rmsd hydrogen bonds : bond 0.05795 ( 414) hydrogen bonds : angle 4.31715 ( 1233) covalent geometry : bond 0.00369 ( 7128) covalent geometry : angle 0.60981 ( 9501) Misc. bond : bond 0.00013 ( 3) *********************** 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: 21 poor density : 68 time to evaluate : 0.749 Fit side-chains REVERT: A 171 ARG cc_start: 0.8131 (ttt-90) cc_final: 0.7539 (ttp-170) REVERT: A 174 LYS cc_start: 0.8737 (mtpm) cc_final: 0.8386 (mtmp) REVERT: A 186 ARG cc_start: 0.8751 (ttt180) cc_final: 0.8227 (ttm110) REVERT: B 5 ASP cc_start: 0.8654 (m-30) cc_final: 0.8414 (m-30) REVERT: B 171 ARG cc_start: 0.8237 (ttt-90) cc_final: 0.7602 (ttp-170) REVERT: B 174 LYS cc_start: 0.8832 (mtpm) cc_final: 0.8445 (mtmm) REVERT: C 171 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7668 (ttp-170) REVERT: C 174 LYS cc_start: 0.8757 (mtpm) cc_final: 0.8415 (mtmp) REVERT: C 252 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7880 (mm-30) outliers start: 21 outliers final: 8 residues processed: 79 average time/residue: 1.5560 time to fit residues: 128.7037 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 : 0.672 ------------------------------------------------------------------------------- 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: 2.9990 chunk 28 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.127515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120592 restraints weight = 6496.582| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.44 r_work: 0.3164 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7131 Z= 0.124 Angle : 0.529 7.336 9501 Z= 0.264 Chirality : 0.039 0.131 927 Planarity : 0.005 0.040 1137 Dihedral : 19.496 144.838 1300 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.12 % Allowed : 7.73 % Favored : 90.15 % 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: 2.48 (0.29), residues: 771 helix: 2.11 (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 0.013 0.001 TRP B 42 HIS 0.002 0.001 HIS A 225 PHE 0.013 0.001 PHE A 134 TYR 0.010 0.001 TYR C 81 ARG 0.002 0.000 ARG C 218 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 414) hydrogen bonds : angle 4.14380 ( 1233) covalent geometry : bond 0.00267 ( 7128) covalent geometry : angle 0.52854 ( 9501) Misc. bond : bond 0.00012 ( 3) *********************** 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 94 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.696 Fit side-chains REVERT: A 171 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7694 (ttp80) REVERT: A 174 LYS cc_start: 0.8780 (mtpm) cc_final: 0.8406 (mtmp) REVERT: A 186 ARG cc_start: 0.8754 (ttt180) cc_final: 0.8159 (ttm110) REVERT: B 5 ASP cc_start: 0.8626 (m-30) cc_final: 0.8389 (m-30) REVERT: B 171 ARG cc_start: 0.8155 (ttt-90) cc_final: 0.7542 (ttp-170) REVERT: B 174 LYS cc_start: 0.8828 (mtpm) cc_final: 0.8420 (mtmm) REVERT: C 171 ARG cc_start: 0.8045 (ttt-90) cc_final: 0.7575 (ttp-170) REVERT: C 174 LYS cc_start: 0.8822 (mtpm) cc_final: 0.8451 (mtmp) REVERT: C 244 ARG cc_start: 0.8979 (mtt90) cc_final: 0.8750 (mtm110) outliers start: 14 outliers final: 5 residues processed: 85 average time/residue: 1.4997 time to fit residues: 133.3247 Evaluate side-chains 78 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.135254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129742 restraints weight = 6624.975| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.36 r_work: 0.3298 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7131 Z= 0.149 Angle : 0.572 7.597 9501 Z= 0.285 Chirality : 0.041 0.136 927 Planarity : 0.005 0.039 1137 Dihedral : 19.346 144.594 1300 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.97 % Allowed : 8.33 % Favored : 89.70 % 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: 2.48 (0.29), residues: 771 helix: 2.14 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.67 (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 A 225 PHE 0.014 0.002 PHE A 134 TYR 0.012 0.002 TYR B 81 ARG 0.002 0.000 ARG A 244 Details of bonding type rmsd hydrogen bonds : bond 0.05426 ( 414) hydrogen bonds : angle 4.21180 ( 1233) covalent geometry : bond 0.00336 ( 7128) covalent geometry : angle 0.57246 ( 9501) Misc. bond : bond 0.00010 ( 3) *********************** 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 87 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.704 Fit side-chains REVERT: A 171 ARG cc_start: 0.8143 (ttt-90) cc_final: 0.7542 (ttp-170) REVERT: A 174 LYS cc_start: 0.8741 (mtpm) cc_final: 0.8388 (mtmp) REVERT: A 186 ARG cc_start: 0.8786 (ttt180) cc_final: 0.8245 (ttm110) REVERT: B 5 ASP cc_start: 0.8635 (m-30) cc_final: 0.8409 (m-30) REVERT: B 171 ARG cc_start: 0.8237 (ttt-90) cc_final: 0.7635 (ttp-170) REVERT: B 174 LYS cc_start: 0.8859 (mtpm) cc_final: 0.8470 (mtmm) REVERT: C 171 ARG cc_start: 0.8103 (ttt-90) cc_final: 0.7651 (ttp-170) REVERT: C 174 LYS cc_start: 0.8791 (mtpm) cc_final: 0.8441 (mtmp) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 1.5794 time to fit residues: 134.8147 Evaluate side-chains 79 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU 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: 0.9990 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.127922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121116 restraints weight = 6424.389| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 0.43 r_work: 0.3176 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7131 Z= 0.125 Angle : 0.522 7.336 9501 Z= 0.261 Chirality : 0.039 0.130 927 Planarity : 0.005 0.036 1137 Dihedral : 18.613 142.706 1300 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.36 % Allowed : 8.94 % Favored : 89.70 % 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: 2.66 (0.29), residues: 771 helix: 2.27 (0.21), residues: 528 sheet: None (None), residues: 0 loop : 0.75 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 42 HIS 0.003 0.001 HIS C 225 PHE 0.014 0.001 PHE A 134 TYR 0.010 0.001 TYR C 81 ARG 0.002 0.000 ARG A 244 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 414) hydrogen bonds : angle 4.10047 ( 1233) covalent geometry : bond 0.00274 ( 7128) covalent geometry : angle 0.52238 ( 9501) Misc. bond : bond 0.00009 ( 3) *********************** 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 86 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.451 Fit side-chains REVERT: A 171 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7469 (ttp-170) REVERT: A 174 LYS cc_start: 0.8793 (mtpm) cc_final: 0.8414 (mtmp) REVERT: B 5 ASP cc_start: 0.8620 (m-30) cc_final: 0.8401 (m-30) REVERT: B 171 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7569 (ttp-170) REVERT: B 174 LYS cc_start: 0.8840 (mtpm) cc_final: 0.8442 (mtmm) REVERT: C 171 ARG cc_start: 0.8058 (ttt-90) cc_final: 0.7592 (ttp-170) REVERT: C 174 LYS cc_start: 0.8803 (mtpm) cc_final: 0.8428 (mtmp) REVERT: C 244 ARG cc_start: 0.8965 (mtt90) cc_final: 0.8759 (mtm110) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 1.9564 time to fit residues: 167.4796 Evaluate side-chains 81 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 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: 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 = 0.3498 r_free = 0.3498 target = 0.134288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128866 restraints weight = 6678.035| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.36 r_work: 0.3329 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7131 Z= 0.157 Angle : 0.582 7.719 9501 Z= 0.291 Chirality : 0.041 0.152 927 Planarity : 0.005 0.037 1137 Dihedral : 18.682 143.425 1300 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.36 % Allowed : 9.24 % 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: 2.48 (0.29), residues: 771 helix: 2.14 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.69 (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 0.013 0.002 TYR B 81 ARG 0.002 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05608 ( 414) hydrogen bonds : angle 4.22214 ( 1233) covalent geometry : bond 0.00357 ( 7128) covalent geometry : angle 0.58173 ( 9501) Misc. bond : bond 0.00011 ( 3) *********************** 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 81 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.689 Fit side-chains REVERT: A 171 ARG cc_start: 0.8075 (ttt-90) cc_final: 0.7469 (ttp-170) REVERT: A 174 LYS cc_start: 0.8700 (mtpm) cc_final: 0.8355 (mtmp) REVERT: B 5 ASP cc_start: 0.8590 (m-30) cc_final: 0.8382 (m-30) REVERT: B 171 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7601 (ttp-170) REVERT: B 174 LYS cc_start: 0.8793 (mtpm) cc_final: 0.8411 (mtmm) REVERT: C 171 ARG cc_start: 0.8077 (ttt-90) cc_final: 0.7642 (ttp-170) REVERT: C 174 LYS cc_start: 0.8724 (mtpm) cc_final: 0.8394 (mtmp) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 1.4165 time to fit residues: 114.3956 Evaluate side-chains 77 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.128788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121871 restraints weight = 6512.709| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 0.44 r_work: 0.3186 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7131 Z= 0.119 Angle : 0.509 7.246 9501 Z= 0.254 Chirality : 0.038 0.128 927 Planarity : 0.005 0.035 1137 Dihedral : 17.986 141.207 1300 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.91 % Allowed : 10.00 % 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: 2.70 (0.29), residues: 771 helix: 2.31 (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 0.013 0.001 TRP B 42 HIS 0.002 0.001 HIS A 225 PHE 0.013 0.001 PHE A 134 TYR 0.009 0.001 TYR C 81 ARG 0.001 0.000 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 414) hydrogen bonds : angle 4.06067 ( 1233) covalent geometry : bond 0.00259 ( 7128) covalent geometry : angle 0.50917 ( 9501) Misc. bond : bond 0.00011 ( 3) *********************** 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 84 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.752 Fit side-chains REVERT: A 171 ARG cc_start: 0.8047 (ttt-90) cc_final: 0.7465 (ttp-170) REVERT: A 174 LYS cc_start: 0.8770 (mtpm) cc_final: 0.8396 (mtmp) REVERT: B 5 ASP cc_start: 0.8605 (m-30) cc_final: 0.8404 (m-30) REVERT: B 171 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7556 (ttp-170) REVERT: B 174 LYS cc_start: 0.8833 (mtpm) cc_final: 0.8435 (mtmm) REVERT: C 171 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7589 (ttp-170) REVERT: C 174 LYS cc_start: 0.8790 (mtpm) cc_final: 0.8411 (mtmp) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 1.4768 time to fit residues: 126.7659 Evaluate side-chains 78 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.134361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128968 restraints weight = 6834.225| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.36 r_work: 0.3329 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7131 Z= 0.160 Angle : 0.583 7.863 9501 Z= 0.292 Chirality : 0.041 0.165 927 Planarity : 0.005 0.038 1137 Dihedral : 18.283 142.727 1300 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.06 % Allowed : 9.70 % 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: 2.48 (0.29), residues: 771 helix: 2.20 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.57 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 42 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.002 PHE A 134 TYR 0.013 0.002 TYR B 81 ARG 0.002 0.001 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.05598 ( 414) hydrogen bonds : angle 4.21602 ( 1233) covalent geometry : bond 0.00365 ( 7128) covalent geometry : angle 0.58320 ( 9501) Misc. bond : bond 0.00006 ( 3) ********************** 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 78 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.702 Fit side-chains REVERT: A 171 ARG cc_start: 0.8099 (ttt-90) cc_final: 0.7495 (ttp-170) REVERT: A 174 LYS cc_start: 0.8697 (mtpm) cc_final: 0.8354 (mtmp) REVERT: B 5 ASP cc_start: 0.8619 (m-30) cc_final: 0.8411 (m-30) REVERT: B 171 ARG cc_start: 0.8231 (ttt-90) cc_final: 0.7614 (ttp-170) REVERT: B 174 LYS cc_start: 0.8809 (mtpm) cc_final: 0.8423 (mtmm) REVERT: C 171 ARG cc_start: 0.8121 (ttt-90) cc_final: 0.7679 (ttp-170) REVERT: C 174 LYS cc_start: 0.8784 (mtpm) cc_final: 0.8452 (mtmp) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 1.4039 time to fit residues: 110.7741 Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 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 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.132481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127185 restraints weight = 6701.318| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 0.35 r_work: 0.3299 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7131 Z= 0.188 Angle : 0.635 8.102 9501 Z= 0.318 Chirality : 0.044 0.187 927 Planarity : 0.005 0.039 1137 Dihedral : 18.746 144.450 1300 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.91 % Allowed : 10.15 % 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: 2.21 (0.28), residues: 771 helix: 1.98 (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 0.002 TRP C 42 HIS 0.004 0.001 HIS A 225 PHE 0.016 0.002 PHE A 134 TYR 0.015 0.002 TYR B 81 ARG 0.003 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.06149 ( 414) hydrogen bonds : angle 4.35556 ( 1233) covalent geometry : bond 0.00436 ( 7128) covalent geometry : angle 0.63534 ( 9501) Misc. bond : bond 0.00016 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5352.11 seconds wall clock time: 94 minutes 26.79 seconds (5666.79 seconds total)