Starting phenix.real_space_refine on Wed Sep 17 06:45:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zao_39882/09_2025/8zao_39882_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zao_39882/09_2025/8zao_39882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zao_39882/09_2025/8zao_39882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zao_39882/09_2025/8zao_39882.map" model { file = "/net/cci-nas-00/data/ceres_data/8zao_39882/09_2025/8zao_39882_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zao_39882/09_2025/8zao_39882_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.008 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 K 15 8.98 5 S 60 5.16 5 C 4326 2.51 5 N 966 2.21 5 O 1065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6432 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2109 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "B" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2109 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "C" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2109 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 25 Unusual residues: {' K': 5, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 25 Unusual residues: {' K': 5, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 25 Unusual residues: {' K': 5, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 1.72, per 1000 atoms: 0.27 Number of scatterers: 6432 At special positions: 0 Unit cell: (74.9, 73.5, 79.45, 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) K 15 19.00 S 60 16.00 O 1065 8.00 N 966 7.00 C 4326 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: 0.57 Conformation dependent library (CDL) restraints added in 376.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1434 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 removed outlier: 3.736A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.740A 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 178 removed outlier: 3.823A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.616A pdb=" N ARG A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.900A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.637A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (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 50 removed outlier: 3.743A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 3.757A 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 178 removed outlier: 3.822A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.588A pdb=" N ARG B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.907A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 3.597A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (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 50 removed outlier: 3.743A pdb=" N GLY C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 3.711A 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 178 removed outlier: 3.821A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.619A pdb=" N ARG C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.900A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 208 removed outlier: 3.632A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (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. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1814 1.35 - 1.46: 1976 1.46 - 1.58: 2768 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 6639 Sorted by residual: bond pdb=" C TRP B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.64e+00 bond pdb=" C TRP A 199 " pdb=" N PRO A 200 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.31e+00 bond pdb=" C TRP C 199 " pdb=" N PRO C 200 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.19e-02 7.06e+03 2.24e+00 bond pdb=" CA PHE C 202 " pdb=" C PHE C 202 " ideal model delta sigma weight residual 1.520 1.532 -0.011 1.23e-02 6.61e+03 8.32e-01 bond pdb=" C PHE A 198 " pdb=" N TRP A 199 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.33e-02 5.65e+03 7.74e-01 ... (remaining 6634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 8835 1.59 - 3.17: 184 3.17 - 4.76: 14 4.76 - 6.35: 12 6.35 - 7.93: 3 Bond angle restraints: 9048 Sorted by residual: angle pdb=" C GLY A 93 " pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta sigma weight residual 120.49 128.42 -7.93 1.42e+00 4.96e-01 3.12e+01 angle pdb=" C GLY B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta sigma weight residual 120.49 128.40 -7.91 1.42e+00 4.96e-01 3.11e+01 angle pdb=" C GLY C 93 " pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta sigma weight residual 120.49 128.40 -7.91 1.42e+00 4.96e-01 3.10e+01 angle pdb=" C TRP B 102 " pdb=" N TYR B 103 " pdb=" CA TYR B 103 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.99e+00 angle pdb=" C TRP C 102 " pdb=" N TYR C 103 " pdb=" CA TYR C 103 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.86e+00 ... (remaining 9043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3266 17.99 - 35.99: 337 35.99 - 53.98: 87 53.98 - 71.97: 12 71.97 - 89.97: 3 Dihedral angle restraints: 3705 sinusoidal: 1449 harmonic: 2256 Sorted by residual: dihedral pdb=" N ARG A 244 " pdb=" CA ARG A 244 " pdb=" CB ARG A 244 " pdb=" CG ARG A 244 " ideal model delta sinusoidal sigma weight residual -180.00 -120.20 -59.80 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG C 244 " pdb=" CA ARG C 244 " pdb=" CB ARG C 244 " pdb=" CG ARG C 244 " ideal model delta sinusoidal sigma weight residual -180.00 -120.32 -59.68 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU C 252 " pdb=" CB GLU C 252 " pdb=" CG GLU C 252 " pdb=" CD GLU C 252 " ideal model delta sinusoidal sigma weight residual -60.00 -119.58 59.58 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 477 0.024 - 0.047: 266 0.047 - 0.071: 121 0.071 - 0.095: 41 0.095 - 0.119: 22 Chirality restraints: 927 Sorted by residual: chirality pdb=" CA TYR A 103 " pdb=" N TYR A 103 " pdb=" C TYR A 103 " pdb=" CB TYR A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA TYR C 103 " pdb=" N TYR C 103 " pdb=" C TYR C 103 " pdb=" CB TYR C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA TYR B 103 " pdb=" N TYR B 103 " pdb=" C TYR B 103 " pdb=" CB TYR B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 924 not shown) Planarity restraints: 1113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 199 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO C 200 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 199 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 200 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 199 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 200 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.032 5.00e-02 4.00e+02 ... (remaining 1110 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 22 2.31 - 3.02: 3718 3.02 - 3.72: 12654 3.72 - 4.43: 21002 4.43 - 5.14: 33112 Nonbonded interactions: 70508 Sorted by model distance: nonbonded pdb=" K K C 302 " pdb=" O HOH C 407 " model vdw 1.601 2.850 nonbonded pdb=" K K B 302 " pdb=" O HOH B 407 " model vdw 1.602 2.850 nonbonded pdb=" K K A 302 " pdb=" O HOH A 407 " model vdw 1.605 2.850 nonbonded pdb=" K K A 304 " pdb=" O HOH A 404 " model vdw 1.995 2.850 nonbonded pdb=" K K B 302 " pdb=" O HOH B 406 " model vdw 2.024 2.850 ... (remaining 70503 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 19.460 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: 0.350 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.570 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.003 0.033 6642 Z= 0.150 Angle : 0.571 7.935 9048 Z= 0.328 Chirality : 0.038 0.119 927 Planarity : 0.006 0.058 1113 Dihedral : 15.637 89.966 2271 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.64 % Allowed : 15.25 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.30), residues: 771 helix: 1.59 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.93 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 62 TYR 0.011 0.001 TYR B 81 PHE 0.011 0.001 PHE C 165 TRP 0.008 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6639) covalent geometry : angle 0.57132 ( 9048) hydrogen bonds : bond 0.13431 ( 414) hydrogen bonds : angle 6.15241 ( 1242) Misc. bond : bond 0.00031 ( 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 85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7604 (mmmt) REVERT: A 178 LEU cc_start: 0.8150 (mt) cc_final: 0.7799 (mm) REVERT: B 14 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7605 (mmmt) REVERT: B 178 LEU cc_start: 0.8130 (mt) cc_final: 0.7774 (mm) REVERT: B 230 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7587 (tp) REVERT: C 14 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7624 (mmmt) REVERT: C 178 LEU cc_start: 0.8170 (mt) cc_final: 0.7787 (mm) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.3587 time to fit residues: 31.4418 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 233 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.107756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.095130 restraints weight = 7166.381| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.50 r_work: 0.3049 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6642 Z= 0.145 Angle : 0.506 5.436 9048 Z= 0.256 Chirality : 0.038 0.121 927 Planarity : 0.005 0.038 1113 Dihedral : 8.760 88.051 901 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.29 % Allowed : 14.05 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.30), residues: 771 helix: 1.81 (0.21), residues: 528 sheet: None (None), residues: 0 loop : 1.02 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 62 TYR 0.010 0.001 TYR A 81 PHE 0.021 0.001 PHE A 144 TRP 0.008 0.001 TRP A 138 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6639) covalent geometry : angle 0.50617 ( 9048) hydrogen bonds : bond 0.04520 ( 414) hydrogen bonds : angle 4.37353 ( 1242) Misc. bond : bond 0.00008 ( 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 110 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7582 (mmmt) REVERT: A 252 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: B 14 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7605 (mptt) REVERT: B 178 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7808 (mm) REVERT: B 183 LYS cc_start: 0.7349 (mtpp) cc_final: 0.7080 (tppp) REVERT: B 230 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7359 (tp) REVERT: B 252 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: C 14 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7592 (mmmt) REVERT: C 178 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7815 (mm) REVERT: C 252 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7614 (mm-30) outliers start: 22 outliers final: 8 residues processed: 100 average time/residue: 0.3944 time to fit residues: 42.4469 Evaluate side-chains 88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS 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 42 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.107879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.094915 restraints weight = 7065.952| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.54 r_work: 0.3028 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6642 Z= 0.123 Angle : 0.471 5.472 9048 Z= 0.235 Chirality : 0.037 0.115 927 Planarity : 0.005 0.039 1113 Dihedral : 8.576 84.410 899 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.74 % Allowed : 14.80 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.29), residues: 771 helix: 1.88 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 0.92 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 62 TYR 0.007 0.001 TYR C 150 PHE 0.014 0.001 PHE A 144 TRP 0.008 0.001 TRP A 138 HIS 0.001 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6639) covalent geometry : angle 0.47111 ( 9048) hydrogen bonds : bond 0.04093 ( 414) hydrogen bonds : angle 4.14482 ( 1242) Misc. bond : bond 0.00012 ( 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 112 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7578 (mptt) REVERT: A 178 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 252 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: B 14 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7600 (mptt) REVERT: B 178 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7791 (mm) REVERT: B 183 LYS cc_start: 0.7265 (mtpp) cc_final: 0.7025 (tppp) REVERT: B 230 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7318 (tp) REVERT: B 252 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: C 14 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7581 (mptt) REVERT: C 178 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7748 (mm) REVERT: C 183 LYS cc_start: 0.7302 (mtpp) cc_final: 0.7037 (tppp) REVERT: C 252 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7645 (mm-30) outliers start: 25 outliers final: 8 residues processed: 102 average time/residue: 0.4242 time to fit residues: 46.1261 Evaluate side-chains 90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS 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 62 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN C 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095386 restraints weight = 7088.880| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.50 r_work: 0.2974 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6642 Z= 0.148 Angle : 0.495 5.498 9048 Z= 0.245 Chirality : 0.038 0.119 927 Planarity : 0.005 0.040 1113 Dihedral : 8.601 85.426 899 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.74 % Allowed : 15.40 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.29), residues: 771 helix: 1.87 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 0.92 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 151 TYR 0.008 0.001 TYR C 180 PHE 0.020 0.001 PHE A 144 TRP 0.008 0.001 TRP C 42 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6639) covalent geometry : angle 0.49518 ( 9048) hydrogen bonds : bond 0.04137 ( 414) hydrogen bonds : angle 4.11983 ( 1242) Misc. bond : bond 0.00027 ( 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 101 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7587 (mptt) REVERT: A 183 LYS cc_start: 0.7286 (mtpp) cc_final: 0.7041 (tppp) REVERT: A 252 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: B 14 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7583 (mptt) REVERT: B 178 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7800 (mm) REVERT: B 183 LYS cc_start: 0.7245 (mtpp) cc_final: 0.7016 (tppp) REVERT: B 230 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7344 (tp) REVERT: B 252 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7768 (mm-30) REVERT: C 14 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7551 (mmmt) REVERT: C 178 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7756 (mm) REVERT: C 183 LYS cc_start: 0.7287 (mtpp) cc_final: 0.7033 (tppp) REVERT: C 252 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7660 (mm-30) outliers start: 25 outliers final: 9 residues processed: 91 average time/residue: 0.4626 time to fit residues: 44.7715 Evaluate side-chains 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS 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 4 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS C 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092736 restraints weight = 7212.435| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.51 r_work: 0.2968 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6642 Z= 0.206 Angle : 0.545 5.569 9048 Z= 0.267 Chirality : 0.040 0.124 927 Planarity : 0.005 0.039 1113 Dihedral : 8.721 89.820 899 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.89 % Allowed : 15.55 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.29), residues: 771 helix: 1.72 (0.21), residues: 534 sheet: None (None), residues: 0 loop : 0.83 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.011 0.002 TYR C 180 PHE 0.020 0.001 PHE C 144 TRP 0.009 0.001 TRP A 42 HIS 0.003 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 6639) covalent geometry : angle 0.54545 ( 9048) hydrogen bonds : bond 0.04507 ( 414) hydrogen bonds : angle 4.22843 ( 1242) Misc. bond : bond 0.00058 ( 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 101 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7562 (mmmt) REVERT: A 183 LYS cc_start: 0.7370 (mtpp) cc_final: 0.7118 (tppp) REVERT: A 252 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: B 14 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7635 (mptt) REVERT: B 230 LEU cc_start: 0.7645 (tp) cc_final: 0.7442 (tp) REVERT: B 252 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: C 14 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7591 (mmmt) REVERT: C 183 LYS cc_start: 0.7369 (mtpp) cc_final: 0.7099 (tppp) REVERT: C 252 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7682 (mm-30) outliers start: 26 outliers final: 10 residues processed: 95 average time/residue: 0.4637 time to fit residues: 46.8027 Evaluate side-chains 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 233 LYS 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 7 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.094858 restraints weight = 7182.450| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.51 r_work: 0.3010 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6642 Z= 0.125 Angle : 0.484 5.511 9048 Z= 0.240 Chirality : 0.037 0.114 927 Planarity : 0.005 0.038 1113 Dihedral : 8.538 86.701 897 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.48 % Allowed : 15.10 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.29), residues: 771 helix: 1.80 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 0.95 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.007 0.001 TYR C 45 PHE 0.022 0.001 PHE B 144 TRP 0.009 0.001 TRP A 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6639) covalent geometry : angle 0.48445 ( 9048) hydrogen bonds : bond 0.04001 ( 414) hydrogen bonds : angle 4.11991 ( 1242) Misc. bond : bond 0.00021 ( 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 106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7550 (mmmt) REVERT: A 178 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7785 (mm) REVERT: A 183 LYS cc_start: 0.7320 (mtpp) cc_final: 0.7080 (tppp) REVERT: A 252 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: B 14 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7602 (mptt) REVERT: B 178 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7818 (mm) REVERT: B 252 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: C 14 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7585 (mmmt) REVERT: C 178 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7776 (mm) REVERT: C 183 LYS cc_start: 0.7330 (mtpp) cc_final: 0.7073 (tppp) REVERT: C 252 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7684 (mm-30) outliers start: 30 outliers final: 9 residues processed: 96 average time/residue: 0.4159 time to fit residues: 42.5619 Evaluate side-chains 83 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS 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 35 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.107313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094537 restraints weight = 7118.350| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.51 r_work: 0.2973 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6642 Z= 0.140 Angle : 0.504 5.783 9048 Z= 0.249 Chirality : 0.038 0.124 927 Planarity : 0.005 0.041 1113 Dihedral : 8.465 82.804 897 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.59 % Allowed : 16.44 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.29), residues: 771 helix: 1.86 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.17 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.008 0.001 TYR B 81 PHE 0.020 0.001 PHE C 144 TRP 0.008 0.001 TRP A 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6639) covalent geometry : angle 0.50426 ( 9048) hydrogen bonds : bond 0.04041 ( 414) hydrogen bonds : angle 4.11203 ( 1242) Misc. bond : bond 0.00038 ( 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 98 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7505 (mmmt) REVERT: A 178 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7704 (mm) REVERT: A 183 LYS cc_start: 0.7199 (mtpp) cc_final: 0.6977 (tppp) REVERT: A 252 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: B 14 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7538 (mptt) REVERT: B 178 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7761 (mm) REVERT: B 252 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7722 (mm-30) REVERT: C 14 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7534 (mmmt) REVERT: C 178 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7712 (mm) REVERT: C 183 LYS cc_start: 0.7219 (mtpp) cc_final: 0.6974 (tppp) REVERT: C 252 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7654 (mm-30) outliers start: 24 outliers final: 12 residues processed: 90 average time/residue: 0.4395 time to fit residues: 42.1399 Evaluate side-chains 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095220 restraints weight = 7106.677| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.50 r_work: 0.3016 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6642 Z= 0.127 Angle : 0.493 6.315 9048 Z= 0.244 Chirality : 0.038 0.131 927 Planarity : 0.005 0.040 1113 Dihedral : 8.439 81.242 897 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.59 % Allowed : 16.29 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.29), residues: 771 helix: 1.93 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.20 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.010 0.001 TYR A 103 PHE 0.023 0.001 PHE A 144 TRP 0.008 0.001 TRP A 42 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6639) covalent geometry : angle 0.49326 ( 9048) hydrogen bonds : bond 0.03947 ( 414) hydrogen bonds : angle 4.08666 ( 1242) Misc. bond : bond 0.00031 ( 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 97 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7560 (mmmt) REVERT: A 178 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7770 (mm) REVERT: A 183 LYS cc_start: 0.7318 (mtpp) cc_final: 0.7101 (tppp) REVERT: A 252 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: B 14 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7612 (mptt) REVERT: B 178 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7827 (mm) REVERT: B 252 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: C 14 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7601 (mmmt) REVERT: C 178 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7778 (mm) REVERT: C 183 LYS cc_start: 0.7333 (mtpp) cc_final: 0.7110 (tppp) REVERT: C 252 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7684 (mm-30) outliers start: 24 outliers final: 11 residues processed: 90 average time/residue: 0.4717 time to fit residues: 45.1602 Evaluate side-chains 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.8644 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.105750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092901 restraints weight = 7269.245| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.49 r_work: 0.2988 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6642 Z= 0.144 Angle : 0.508 6.415 9048 Z= 0.252 Chirality : 0.039 0.137 927 Planarity : 0.005 0.042 1113 Dihedral : 8.473 80.294 897 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.69 % Allowed : 16.89 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.29), residues: 771 helix: 1.91 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.20 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.008 0.001 TYR B 81 PHE 0.017 0.001 PHE C 144 TRP 0.008 0.001 TRP B 42 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6639) covalent geometry : angle 0.50798 ( 9048) hydrogen bonds : bond 0.04068 ( 414) hydrogen bonds : angle 4.10398 ( 1242) Misc. bond : bond 0.00047 ( 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 93 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7562 (mmmt) REVERT: A 178 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7772 (mm) REVERT: A 183 LYS cc_start: 0.7288 (mtpp) cc_final: 0.7076 (tppp) REVERT: A 252 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: B 14 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7604 (mptt) REVERT: B 178 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7822 (mm) REVERT: B 252 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: C 14 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7596 (mmmt) REVERT: C 178 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7775 (mm) REVERT: C 183 LYS cc_start: 0.7314 (mtpp) cc_final: 0.7094 (tppp) REVERT: C 252 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7698 (mm-30) outliers start: 18 outliers final: 10 residues processed: 87 average time/residue: 0.4904 time to fit residues: 45.2392 Evaluate side-chains 88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 1 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.109744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097003 restraints weight = 7019.762| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.51 r_work: 0.3024 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6642 Z= 0.117 Angle : 0.484 6.917 9048 Z= 0.241 Chirality : 0.038 0.130 927 Planarity : 0.005 0.042 1113 Dihedral : 8.331 77.789 897 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.54 % Allowed : 16.74 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.30), residues: 771 helix: 2.00 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.19 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 151 TYR 0.007 0.001 TYR C 45 PHE 0.012 0.001 PHE A 144 TRP 0.008 0.001 TRP B 42 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6639) covalent geometry : angle 0.48385 ( 9048) hydrogen bonds : bond 0.03855 ( 414) hydrogen bonds : angle 4.06836 ( 1242) Misc. bond : bond 0.00045 ( 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 94 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7543 (mmmt) REVERT: A 178 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7745 (mm) REVERT: A 183 LYS cc_start: 0.7269 (mtpp) cc_final: 0.7068 (tppp) REVERT: A 252 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: B 14 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7608 (mptt) REVERT: B 178 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 252 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: C 14 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7573 (mmmt) REVERT: C 178 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7733 (mm) REVERT: C 183 LYS cc_start: 0.7287 (mtpp) cc_final: 0.7082 (tppp) REVERT: C 252 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7675 (mt-10) outliers start: 17 outliers final: 10 residues processed: 89 average time/residue: 0.4969 time to fit residues: 46.9204 Evaluate side-chains 89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095366 restraints weight = 7112.067| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.51 r_work: 0.3019 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6642 Z= 0.144 Angle : 0.512 6.730 9048 Z= 0.256 Chirality : 0.039 0.154 927 Planarity : 0.005 0.042 1113 Dihedral : 8.051 77.557 897 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.69 % Allowed : 16.44 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.29), residues: 771 helix: 1.98 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.15 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 151 TYR 0.008 0.001 TYR A 180 PHE 0.019 0.001 PHE A 144 TRP 0.008 0.001 TRP A 138 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6639) covalent geometry : angle 0.51192 ( 9048) hydrogen bonds : bond 0.04089 ( 414) hydrogen bonds : angle 4.11961 ( 1242) Misc. bond : bond 0.00060 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2758.68 seconds wall clock time: 47 minutes 56.31 seconds (2876.31 seconds total)