Starting phenix.real_space_refine on Thu Jul 2 03:23:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zao_39882/07_2026/8zao_39882_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zao_39882/07_2026/8zao_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_39882/07_2026/8zao_39882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zao_39882/07_2026/8zao_39882.map" model { file = "/net/cci-nas-00/data/ceres_data/8zao_39882/07_2026/8zao_39882_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zao_39882/07_2026/8zao_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-dev-6108/lib/python3.11/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, 20 Ad-hoc single atom residues: {' K': 5} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 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, 20 Ad-hoc single atom residues: {' K': 5} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 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, 20 Ad-hoc single atom residues: {' K': 5} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 1.14, per 1000 atoms: 0.18 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: 0.33 Conformation dependent library (CDL) restraints added in 243.0 milliseconds 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: 0.09 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: 0.68 Time building geometry restraints manager: 0.50 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 3.590 nonbonded pdb=" K K B 302 " pdb=" O HOH B 407 " model vdw 1.602 3.590 nonbonded pdb=" K K A 302 " pdb=" O HOH A 407 " model vdw 1.605 3.590 nonbonded pdb=" K K A 304 " pdb=" O HOH A 404 " model vdw 1.995 3.590 nonbonded pdb=" K K B 302 " pdb=" O HOH B 406 " model vdw 2.024 3.590 ... (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: 0.01 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: 19.710 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.500 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:5.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 are 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/Z covalent geometry : bond 0.00315 / 0.15 ( 6639) covalent geometry : angle 0.57132 / 0.33 ( 9048) hydrogen bonds : bond 0.13431 / 9.63 ( 414) hydrogen bonds : angle 6.15241 / 4.21 ( 1242) Misc. bond : bond 0.00031 / 0.02 ( 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 : 0.170 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: 0.2453 time to fit residues: 21.5771 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 : 0.190 ------------------------------------------------------------------------------- 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: 0.5980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.097312 restraints weight = 6783.072| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.41 r_work: 0.3068 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6642 Z= 0.147 Angle : 0.511 5.434 9048 Z= 0.258 Chirality : 0.038 0.118 927 Planarity : 0.005 0.038 1113 Dihedral : 8.760 87.832 901 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.14 % Allowed : 14.20 % 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 are not related in a simple way. whole: 2.28 (0.30), residues: 771 helix: 1.84 (0.21), residues: 528 sheet: None (None), residues: 0 loop : 0.98 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 171 TYR 0.009 0.001 TYR A 81 PHE 0.019 0.001 PHE A 144 TRP 0.008 0.001 TRP A 42 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 6639) covalent geometry : angle 0.51054 / 0.26 ( 9048) hydrogen bonds : bond 0.04543 / 3.16 ( 414) hydrogen bonds : angle 4.37169 / 2.93 ( 1242) Misc. bond : bond 0.00006 / 0.00 ( 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 113 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7598 (mmmt) REVERT: A 252 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7623 (mm-30) REVERT: B 14 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7614 (mptt) REVERT: B 178 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7809 (mm) REVERT: B 183 LYS cc_start: 0.7378 (mtpp) cc_final: 0.7104 (tppp) REVERT: B 230 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7389 (tp) REVERT: B 252 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: C 14 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7598 (mmmt) REVERT: C 178 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7833 (mm) REVERT: C 252 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7630 (mm-30) outliers start: 21 outliers final: 8 residues processed: 104 average time/residue: 0.3140 time to fit residues: 35.0688 Evaluate side-chains 89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN B 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095008 restraints weight = 6827.850| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.39 r_work: 0.3019 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6642 Z= 0.195 Angle : 0.531 5.501 9048 Z= 0.263 Chirality : 0.040 0.126 927 Planarity : 0.005 0.038 1113 Dihedral : 8.740 89.182 899 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.74 % Allowed : 14.50 % Favored : 81.76 % 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 are not related in a simple way. whole: 2.24 (0.29), residues: 771 helix: 1.80 (0.21), residues: 528 sheet: None (None), residues: 0 loop : 0.99 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 62 TYR 0.010 0.002 TYR C 180 PHE 0.018 0.001 PHE A 144 TRP 0.009 0.001 TRP B 42 HIS 0.003 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 6639) covalent geometry : angle 0.53137 / 0.26 ( 9048) hydrogen bonds : bond 0.04615 / 3.23 ( 414) hydrogen bonds : angle 4.28199 / 2.88 ( 1242) Misc. bond : bond 0.00037 / 0.02 ( 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 106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7689 (mptt) REVERT: A 252 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: B 14 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7701 (mptt) REVERT: B 183 LYS cc_start: 0.7498 (mtpp) cc_final: 0.7222 (tppp) REVERT: B 230 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7527 (tp) REVERT: B 252 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: C 14 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7652 (mmmt) REVERT: C 183 LYS cc_start: 0.7518 (mtpp) cc_final: 0.7222 (tppp) REVERT: C 252 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7681 (mm-30) outliers start: 25 outliers final: 10 residues processed: 96 average time/residue: 0.3491 time to fit residues: 35.7656 Evaluate side-chains 93 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3197 r_free = 0.3197 target = 0.105070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.091467 restraints weight = 6973.611| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.43 r_work: 0.2947 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6642 Z= 0.232 Angle : 0.567 5.526 9048 Z= 0.278 Chirality : 0.041 0.126 927 Planarity : 0.005 0.037 1113 Dihedral : 8.583 87.533 899 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 are not related in a simple way. whole: 1.94 (0.29), residues: 771 helix: 1.58 (0.20), residues: 531 sheet: None (None), residues: 0 loop : 0.86 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 128 TYR 0.011 0.002 TYR C 180 PHE 0.028 0.002 PHE A 144 TRP 0.010 0.001 TRP C 42 HIS 0.003 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 ( 6639) covalent geometry : angle 0.56729 / 0.28 ( 9048) hydrogen bonds : bond 0.04736 / 3.32 ( 414) hydrogen bonds : angle 4.31741 / 2.91 ( 1242) Misc. bond : bond 0.00065 / 0.04 ( 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 105 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7606 (mptt) REVERT: A 183 LYS cc_start: 0.7314 (mtpp) cc_final: 0.7018 (tppp) REVERT: A 252 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: B 14 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7617 (mptt) REVERT: B 183 LYS cc_start: 0.7304 (mtpp) cc_final: 0.7025 (tppp) REVERT: B 230 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7415 (tp) REVERT: B 252 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: C 14 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7531 (mmmt) REVERT: C 183 LYS cc_start: 0.7332 (mtpp) cc_final: 0.7034 (tppp) outliers start: 25 outliers final: 12 residues processed: 96 average time/residue: 0.3286 time to fit residues: 33.5856 Evaluate side-chains 97 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.094966 restraints weight = 6975.090| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.47 r_work: 0.3005 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6642 Z= 0.146 Angle : 0.505 5.499 9048 Z= 0.248 Chirality : 0.038 0.115 927 Planarity : 0.005 0.036 1113 Dihedral : 8.644 87.340 899 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.44 % Allowed : 15.84 % 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 are not related in a simple way. whole: 2.00 (0.29), residues: 771 helix: 1.66 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 0.76 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 128 TYR 0.009 0.001 TYR B 81 PHE 0.023 0.001 PHE B 144 TRP 0.010 0.001 TRP B 42 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 6639) covalent geometry : angle 0.50539 / 0.25 ( 9048) hydrogen bonds : bond 0.04199 / 2.92 ( 414) hydrogen bonds : angle 4.19477 / 2.83 ( 1242) Misc. bond : bond 0.00033 / 0.02 ( 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 105 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7594 (mmmt) REVERT: A 183 LYS cc_start: 0.7390 (mtpp) cc_final: 0.7113 (tppp) REVERT: A 252 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: B 14 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7661 (mptt) REVERT: B 183 LYS cc_start: 0.7388 (mtpp) cc_final: 0.7123 (tppp) REVERT: B 252 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: C 14 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7609 (mmmt) REVERT: C 178 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7824 (mm) REVERT: C 183 LYS cc_start: 0.7411 (mtpp) cc_final: 0.7133 (tppp) outliers start: 23 outliers final: 9 residues processed: 96 average time/residue: 0.3559 time to fit residues: 36.3124 Evaluate side-chains 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain C residue 233 LYS 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: 0.3980 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096282 restraints weight = 6943.521| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.48 r_work: 0.3029 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1250 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= 0.129 Angle : 0.487 5.485 9048 Z= 0.240 Chirality : 0.037 0.115 927 Planarity : 0.005 0.037 1113 Dihedral : 8.586 89.874 897 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.04 % Allowed : 15.10 % 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 are not related in a simple way. whole: 2.33 (0.30), residues: 771 helix: 1.85 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.04 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 151 TYR 0.007 0.001 TYR C 45 PHE 0.018 0.001 PHE C 144 TRP 0.009 0.001 TRP C 42 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6639) covalent geometry : angle 0.48697 / 0.24 ( 9048) hydrogen bonds : bond 0.04029 / 2.79 ( 414) hydrogen bonds : angle 4.12166 / 2.77 ( 1242) Misc. bond : bond 0.00023 / 0.02 ( 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 109 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7612 (mmmt) REVERT: A 183 LYS cc_start: 0.7398 (mtpp) cc_final: 0.7144 (tppp) REVERT: A 252 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: B 14 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7651 (mptt) REVERT: B 178 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7881 (mm) REVERT: B 183 LYS cc_start: 0.7410 (mtpp) cc_final: 0.7168 (tppp) REVERT: B 252 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: C 14 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7626 (mmmt) REVERT: C 178 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7836 (mm) REVERT: C 183 LYS cc_start: 0.7412 (mtpp) cc_final: 0.7149 (tppp) outliers start: 27 outliers final: 9 residues processed: 102 average time/residue: 0.3431 time to fit residues: 37.4042 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 : 0.141 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain C residue 233 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.093548 restraints weight = 6914.894| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.47 r_work: 0.2993 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.005 0.034 6642 Z= 0.191 Angle : 0.540 5.553 9048 Z= 0.266 Chirality : 0.040 0.124 927 Planarity : 0.005 0.039 1113 Dihedral : 8.606 88.842 897 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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 are not related in a simple way. whole: 2.18 (0.29), residues: 771 helix: 1.76 (0.21), residues: 534 sheet: None (None), residues: 0 loop : 0.93 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 151 TYR 0.011 0.002 TYR C 180 PHE 0.026 0.001 PHE B 144 TRP 0.009 0.001 TRP A 42 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 ( 6639) covalent geometry : angle 0.54014 / 0.27 ( 9048) hydrogen bonds : bond 0.04390 / 3.06 ( 414) hydrogen bonds : angle 4.20483 / 2.83 ( 1242) Misc. bond : bond 0.00051 / 0.03 ( 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 105 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7620 (mmmt) REVERT: A 183 LYS cc_start: 0.7477 (mtpp) cc_final: 0.7225 (tppp) REVERT: B 14 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7674 (mptt) REVERT: B 183 LYS cc_start: 0.7468 (mtpp) cc_final: 0.7220 (tppp) REVERT: B 252 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: C 14 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7629 (mmmt) REVERT: C 178 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7866 (mm) REVERT: C 183 LYS cc_start: 0.7469 (mtpp) cc_final: 0.7202 (tppp) outliers start: 26 outliers final: 13 residues processed: 98 average time/residue: 0.3393 time to fit residues: 35.5021 Evaluate side-chains 94 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 221 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 LYS 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 59 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 LYS 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: 0.6980 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096974 restraints weight = 6773.247| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.47 r_work: 0.3035 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6642 Z= 0.123 Angle : 0.483 5.509 9048 Z= 0.240 Chirality : 0.037 0.127 927 Planarity : 0.005 0.041 1113 Dihedral : 8.523 86.911 897 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.84 % Allowed : 16.74 % 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 are not related in a simple way. whole: 2.40 (0.30), residues: 771 helix: 1.90 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.07 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 151 TYR 0.008 0.001 TYR C 45 PHE 0.015 0.001 PHE B 144 TRP 0.009 0.001 TRP A 42 HIS 0.001 0.000 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6639) covalent geometry : angle 0.48290 / 0.24 ( 9048) hydrogen bonds : bond 0.03938 / 2.72 ( 414) hydrogen bonds : angle 4.11068 / 2.77 ( 1242) Misc. bond : bond 0.00025 / 0.02 ( 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 102 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7621 (mmmt) REVERT: A 178 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 183 LYS cc_start: 0.7409 (mtpp) cc_final: 0.7161 (tppp) REVERT: B 14 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7662 (mptt) REVERT: B 178 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7875 (mm) REVERT: B 183 LYS cc_start: 0.7417 (mtpp) cc_final: 0.7179 (tppp) REVERT: B 252 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: C 14 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7641 (mmmt) REVERT: C 178 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7830 (mm) REVERT: C 183 LYS cc_start: 0.7416 (mtpp) cc_final: 0.7157 (tppp) outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 0.4453 time to fit residues: 45.1774 Evaluate side-chains 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 178 LEU Chi-restraints excluded: chain C residue 233 LYS 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: 0.9990 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.096912 restraints weight = 6809.601| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.48 r_work: 0.3015 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6642 Z= 0.130 Angle : 0.493 5.490 9048 Z= 0.246 Chirality : 0.038 0.126 927 Planarity : 0.005 0.041 1113 Dihedral : 8.451 81.059 897 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.69 % Allowed : 16.74 % 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 are not related in a simple way. whole: 2.45 (0.30), residues: 771 helix: 1.94 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.08 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 151 TYR 0.009 0.001 TYR A 103 PHE 0.018 0.001 PHE B 144 TRP 0.008 0.001 TRP A 42 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6639) covalent geometry : angle 0.49327 / 0.25 ( 9048) hydrogen bonds : bond 0.03984 / 2.76 ( 414) hydrogen bonds : angle 4.10482 / 2.76 ( 1242) Misc. bond : bond 0.00031 / 0.02 ( 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 97 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7561 (mmmt) REVERT: A 178 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7763 (mm) REVERT: A 183 LYS cc_start: 0.7288 (mtpp) cc_final: 0.7056 (tppp) REVERT: B 14 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7611 (mptt) REVERT: B 178 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7802 (mm) REVERT: B 183 LYS cc_start: 0.7298 (mtpp) cc_final: 0.7085 (tppp) REVERT: B 252 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: C 14 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7591 (mmmt) REVERT: C 178 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7755 (mm) REVERT: C 183 LYS cc_start: 0.7313 (mtpp) cc_final: 0.7070 (tppp) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.4485 time to fit residues: 43.4610 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 : 0.250 ------------------------------------------------------------------------------- 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 221 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 LYS 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 178 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 0.0040 chunk 23 optimal weight: 0.0470 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.0060 chunk 29 optimal weight: 1.9990 overall best weight: 0.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.099456 restraints weight = 6698.041| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.51 r_work: 0.3079 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6642 Z= 0.104 Angle : 0.464 5.422 9048 Z= 0.234 Chirality : 0.037 0.135 927 Planarity : 0.005 0.041 1113 Dihedral : 8.400 76.121 897 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.39 % Allowed : 16.89 % 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 are not related in a simple way. whole: 2.62 (0.30), residues: 771 helix: 2.10 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.06 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 151 TYR 0.008 0.001 TYR C 45 PHE 0.011 0.001 PHE B 134 TRP 0.010 0.001 TRP B 210 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 6639) covalent geometry : angle 0.46354 / 0.23 ( 9048) hydrogen bonds : bond 0.03687 / 2.52 ( 414) hydrogen bonds : angle 4.03253 / 2.70 ( 1242) Misc. bond : bond 0.00026 / 0.02 ( 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 102 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7666 (mptt) REVERT: A 178 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7794 (mm) REVERT: B 14 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7677 (mptt) REVERT: B 94 THR cc_start: 0.7214 (m) cc_final: 0.6746 (p) REVERT: B 178 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7826 (mm) REVERT: B 183 LYS cc_start: 0.7351 (mtpp) cc_final: 0.7125 (tppp) REVERT: B 252 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: C 14 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7625 (mmmt) REVERT: C 94 THR cc_start: 0.7220 (m) cc_final: 0.6749 (p) REVERT: C 178 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7763 (mm) REVERT: C 183 LYS cc_start: 0.7371 (mtpp) cc_final: 0.7170 (tppp) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 0.4742 time to fit residues: 48.3935 Evaluate side-chains 92 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 B residue 3 PHE 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 230 LEU Chi-restraints excluded: chain C residue 233 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3277 r_free = 0.3277 target = 0.111398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.097806 restraints weight = 6737.633| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.45 r_work: 0.3014 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6642 Z= 0.140 Angle : 0.502 5.498 9048 Z= 0.253 Chirality : 0.039 0.159 927 Planarity : 0.005 0.042 1113 Dihedral : 8.163 76.187 897 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.24 % Allowed : 16.74 % Favored : 81.02 % 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 are not related in a simple way. whole: 2.63 (0.30), residues: 771 helix: 2.11 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.05 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 186 TYR 0.008 0.001 TYR A 180 PHE 0.016 0.001 PHE B 144 TRP 0.008 0.001 TRP A 138 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6639) covalent geometry : angle 0.50245 / 0.25 ( 9048) hydrogen bonds : bond 0.04041 / 2.79 ( 414) hydrogen bonds : angle 4.09221 / 2.75 ( 1242) Misc. bond : bond 0.00059 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.35 seconds wall clock time: 40 minutes 25.92 seconds (2425.92 seconds total)