Starting phenix.real_space_refine on Tue Aug 4 23:00:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h86_34530/08_2026/8h86_34530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h86_34530/08_2026/8h86_34530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2026/8h86_34530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2026/8h86_34530.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2026/8h86_34530.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2026/8h86_34530.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2026/8h86_34530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2026/8h86_34530.cif" } resolution = 2.56 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= 0.002 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 60 5.16 5 C 4896 2.51 5 N 957 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7080 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2090 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2071 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2071 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2129 Chain: "A" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 270 Unusual residues: {'PLM': 5, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 16, 'water': 21} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-3': 6, 'PSC:plan-4': 6, 'PLM:plan-1': 5, 'PSC:plan-1': 6, 'PSC:plan-2': 6} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Restraints were copied for chains: B, C Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N APHE A 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 144 " occ=0.50 residue: pdb=" N APHE B 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 144 " occ=0.50 residue: pdb=" N APHE C 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 144 " occ=0.50 Time building chain proxies: 2.12, per 1000 atoms: 0.30 Number of scatterers: 7080 At special positions: 0 Unit cell: (78.02, 76.36, 82.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 9 15.00 O 1158 8.00 N 957 7.00 C 4896 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: 0.62 Conformation dependent library (CDL) restraints added in 564.8 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: 1422 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 49 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.992A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.802A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.003A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.663A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 252 removed outlier: 3.633A pdb=" N ILE A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 49 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 103 through 122 removed outlier: 3.992A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.802A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.003A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.663A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 252 removed outlier: 3.634A pdb=" N ILE B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE B 236 " --> pdb=" O CYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 49 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 103 through 122 removed outlier: 3.992A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.802A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.003A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.663A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 252 removed outlier: 3.633A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE C 236 " --> pdb=" O CYS C 232 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1305 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: 0.96 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1031 1.32 - 1.45: 2428 1.45 - 1.58: 3672 1.58 - 1.71: 15 1.71 - 1.84: 81 Bond restraints: 7227 Sorted by residual: bond pdb=" C7 PSC A 311 " pdb=" C8 PSC A 311 " ideal model delta sigma weight residual 1.530 1.322 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C7 PSC C 311 " pdb=" C8 PSC C 311 " ideal model delta sigma weight residual 1.530 1.322 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C7 PSC B 311 " pdb=" C8 PSC B 311 " ideal model delta sigma weight residual 1.530 1.323 0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C6 PSC A 313 " pdb=" C7 PSC A 313 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C6 PSC C 313 " pdb=" C7 PSC C 313 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.05e+02 ... (remaining 7222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 9173 2.95 - 5.91: 403 5.91 - 8.86: 15 8.86 - 11.82: 21 11.82 - 14.77: 21 Bond angle restraints: 9633 Sorted by residual: angle pdb=" C10 PSC C 311 " pdb=" C11 PSC C 311 " pdb=" C12 PSC C 311 " ideal model delta sigma weight residual 111.07 125.84 -14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C10 PSC A 311 " pdb=" C11 PSC A 311 " pdb=" C12 PSC A 311 " ideal model delta sigma weight residual 111.07 125.82 -14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C10 PSC B 311 " pdb=" C11 PSC B 311 " pdb=" C12 PSC B 311 " ideal model delta sigma weight residual 111.07 125.82 -14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C2 PSC B 312 " pdb=" C3 PSC B 312 " pdb=" C4 PSC B 312 " ideal model delta sigma weight residual 111.73 125.94 -14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" C2 PSC C 312 " pdb=" C3 PSC C 312 " pdb=" C4 PSC C 312 " ideal model delta sigma weight residual 111.73 125.93 -14.20 3.00e+00 1.11e-01 2.24e+01 ... (remaining 9628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.23: 3761 25.23 - 50.45: 298 50.45 - 75.68: 48 75.68 - 100.90: 0 100.90 - 126.12: 6 Dihedral angle restraints: 4113 sinusoidal: 1872 harmonic: 2241 Sorted by residual: dihedral pdb=" C02 PSC C 303 " pdb=" C03 PSC C 303 " pdb=" O11 PSC C 303 " pdb=" P PSC C 303 " ideal model delta sinusoidal sigma weight residual 180.62 54.50 126.12 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C02 PSC B 303 " pdb=" C03 PSC B 303 " pdb=" O11 PSC B 303 " pdb=" P PSC B 303 " ideal model delta sinusoidal sigma weight residual 180.62 54.51 126.11 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C02 PSC A 303 " pdb=" C03 PSC A 303 " pdb=" O11 PSC A 303 " pdb=" P PSC A 303 " ideal model delta sinusoidal sigma weight residual 180.62 54.54 126.08 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 4110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 458 0.052 - 0.105: 299 0.105 - 0.157: 109 0.157 - 0.209: 58 0.209 - 0.261: 9 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA TYR B 81 " pdb=" N TYR B 81 " pdb=" C TYR B 81 " pdb=" CB TYR B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA TYR C 81 " pdb=" N TYR C 81 " pdb=" C TYR C 81 " pdb=" CB TYR C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA TYR A 81 " pdb=" N TYR A 81 " pdb=" C TYR A 81 " pdb=" CB TYR A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 930 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 PSC B 311 " 0.268 2.00e-02 2.50e+03 2.81e-01 7.87e+02 pdb=" C12 PSC B 311 " -0.238 2.00e-02 2.50e+03 pdb=" C13 PSC B 311 " -0.320 2.00e-02 2.50e+03 pdb=" C14 PSC B 311 " 0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PSC C 311 " -0.268 2.00e-02 2.50e+03 2.80e-01 7.87e+02 pdb=" C12 PSC C 311 " 0.238 2.00e-02 2.50e+03 pdb=" C13 PSC C 311 " 0.320 2.00e-02 2.50e+03 pdb=" C14 PSC C 311 " -0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PSC A 311 " -0.268 2.00e-02 2.50e+03 2.80e-01 7.86e+02 pdb=" C12 PSC A 311 " 0.238 2.00e-02 2.50e+03 pdb=" C13 PSC A 311 " 0.320 2.00e-02 2.50e+03 pdb=" C14 PSC A 311 " -0.289 2.00e-02 2.50e+03 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1904 2.82 - 3.34: 6804 3.34 - 3.86: 12425 3.86 - 4.38: 15633 4.38 - 4.90: 25093 Nonbonded interactions: 61859 Sorted by model distance: nonbonded pdb=" OG SER A 68 " pdb=" O HOH A 401 " model vdw 2.296 3.040 nonbonded pdb=" OG SER C 68 " pdb=" O HOH C 401 " model vdw 2.296 3.040 nonbonded pdb=" OG SER B 68 " pdb=" O HOH B 401 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR A 146 " pdb=" O HOH A 402 " model vdw 2.385 3.040 nonbonded pdb=" NH2 ARG C 171 " pdb=" O13 PSC C 310 " model vdw 2.385 3.120 ... (remaining 61854 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.040 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 0.015 0.208 7230 Z= 0.868 Angle : 1.563 14.769 9633 Z= 0.928 Chirality : 0.082 0.261 933 Planarity : 0.030 0.281 1155 Dihedral : 17.742 126.125 2691 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.45 % Allowed : 2.26 % Favored : 97.29 % 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: -0.67 (0.28), residues: 771 helix: -0.49 (0.18), residues: 537 sheet: None (None), residues: 0 loop : 0.15 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG C 62 TYR 0.043 0.009 TYR C 155 PHE 0.047 0.010 PHE A 86 TRP 0.047 0.009 TRP B 190 HIS 0.014 0.004 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.01434 / 0.80 ( 7227) covalent geometry : angle 1.56274 / 0.93 ( 9633) hydrogen bonds : bond 0.19337 / 12.91 ( 438) hydrogen bonds : angle 7.43519 / 5.48 ( 1305) Misc. bond : bond 0.16901 / 8.47 ( 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 97 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.166 Fit side-chains REVERT: A 20 MET cc_start: 0.7679 (mtm) cc_final: 0.7391 (mtm) REVERT: A 170 MET cc_start: 0.6515 (mtm) cc_final: 0.6266 (mtt) REVERT: B 60 SER cc_start: 0.7505 (m) cc_final: 0.7289 (t) REVERT: B 170 MET cc_start: 0.6548 (mtm) cc_final: 0.6181 (mtt) REVERT: B 186 ARG cc_start: 0.6295 (ttm170) cc_final: 0.5676 (ttt180) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.6970 time to fit residues: 70.6186 Evaluate side-chains 85 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107868 restraints weight = 23562.758| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.06 r_work: 0.2784 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7230 Z= 0.137 Angle : 0.593 8.695 9633 Z= 0.293 Chirality : 0.041 0.127 933 Planarity : 0.005 0.033 1155 Dihedral : 17.810 90.698 1314 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.21 % Allowed : 4.52 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.75 (0.30), residues: 771 helix: 2.11 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 1.30 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 171 TYR 0.013 0.001 TYR C 81 PHE 0.024 0.002 PHE C 221 TRP 0.022 0.002 TRP B 42 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 7227) covalent geometry : angle 0.59270 / 0.29 ( 9633) hydrogen bonds : bond 0.05415 / 3.53 ( 438) hydrogen bonds : angle 4.29781 / 3.21 ( 1305) Misc. bond : bond 0.00072 / 0.04 ( 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 88 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.255 Fit side-chains REVERT: A 170 MET cc_start: 0.8711 (mtm) cc_final: 0.8398 (mtt) REVERT: A 248 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8479 (mt-10) REVERT: B 170 MET cc_start: 0.8813 (mtm) cc_final: 0.8435 (mtt) REVERT: B 171 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8309 (ttp80) outliers start: 5 outliers final: 0 residues processed: 83 average time/residue: 0.6754 time to fit residues: 58.8140 Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.134539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103865 restraints weight = 22783.450| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.04 r_work: 0.2936 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7230 Z= 0.178 Angle : 0.609 7.164 9633 Z= 0.306 Chirality : 0.043 0.130 933 Planarity : 0.005 0.049 1155 Dihedral : 16.734 72.178 1314 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.21 % Allowed : 5.73 % Favored : 93.06 % 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: 2.77 (0.30), residues: 771 helix: 2.16 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 1.21 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 171 TYR 0.017 0.002 TYR C 81 PHE 0.021 0.002 PHE A 221 TRP 0.020 0.002 TRP B 42 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 7227) covalent geometry : angle 0.60945 / 0.31 ( 9633) hydrogen bonds : bond 0.06323 / 4.12 ( 438) hydrogen bonds : angle 4.27763 / 3.18 ( 1305) Misc. bond : bond 0.00112 / 0.06 ( 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 81 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.179 Fit side-chains REVERT: A 56 LYS cc_start: 0.7998 (tttp) cc_final: 0.7705 (tttt) REVERT: A 174 LYS cc_start: 0.8498 (tttp) cc_final: 0.8007 (ttpt) REVERT: A 186 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6717 (tmm-80) REVERT: B 170 MET cc_start: 0.8774 (mtm) cc_final: 0.8354 (mtt) REVERT: B 171 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8321 (ttp80) outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 0.6913 time to fit residues: 56.2444 Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain C residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 0.0170 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN B 218 GLN C 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108588 restraints weight = 21633.259| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.96 r_work: 0.3017 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7230 Z= 0.115 Angle : 0.508 7.054 9633 Z= 0.251 Chirality : 0.038 0.121 933 Planarity : 0.005 0.034 1155 Dihedral : 14.099 59.093 1314 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.66 % Allowed : 5.88 % Favored : 92.46 % 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 are not related in a simple way. whole: 3.30 (0.30), residues: 771 helix: 2.60 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 1.27 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 171 TYR 0.012 0.001 TYR C 81 PHE 0.016 0.001 PHE C 134 TRP 0.018 0.002 TRP A 42 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7227) covalent geometry : angle 0.50832 / 0.25 ( 9633) hydrogen bonds : bond 0.04591 / 2.99 ( 438) hydrogen bonds : angle 3.88309 / 2.90 ( 1305) Misc. bond : bond 0.00052 / 0.03 ( 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 88 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.254 Fit side-chains REVERT: A 56 LYS cc_start: 0.8178 (tttp) cc_final: 0.7871 (tttt) REVERT: A 170 MET cc_start: 0.8700 (mtp) cc_final: 0.8437 (mtt) REVERT: A 174 LYS cc_start: 0.8451 (tttp) cc_final: 0.8243 (tmtp) REVERT: A 186 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6716 (tmm-80) REVERT: B 170 MET cc_start: 0.8810 (mtm) cc_final: 0.8386 (mtt) REVERT: B 171 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8408 (ttp80) REVERT: C 174 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7897 (ttpt) outliers start: 8 outliers final: 3 residues processed: 85 average time/residue: 0.7438 time to fit residues: 65.8501 Evaluate side-chains 77 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS B 215 HIS C 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.104113 restraints weight = 19387.885| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.86 r_work: 0.2908 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7230 Z= 0.156 Angle : 0.564 6.779 9633 Z= 0.280 Chirality : 0.041 0.127 933 Planarity : 0.005 0.048 1155 Dihedral : 13.943 59.928 1314 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.81 % Allowed : 6.64 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.97 (0.30), residues: 771 helix: 2.41 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.97 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 171 TYR 0.016 0.001 TYR A 81 PHE 0.017 0.002 PHE C 134 TRP 0.017 0.002 TRP B 42 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7227) covalent geometry : angle 0.56438 / 0.28 ( 9633) hydrogen bonds : bond 0.05759 / 3.75 ( 438) hydrogen bonds : angle 4.06100 / 3.02 ( 1305) Misc. bond : bond 0.00088 / 0.04 ( 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 86 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.310 Fit side-chains REVERT: A 56 LYS cc_start: 0.8173 (tttp) cc_final: 0.7862 (tttt) REVERT: A 170 MET cc_start: 0.8672 (mtp) cc_final: 0.8402 (mtt) REVERT: A 174 LYS cc_start: 0.8462 (tttp) cc_final: 0.8258 (tmtp) REVERT: A 186 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6723 (tmm-80) REVERT: B 170 MET cc_start: 0.8820 (mtm) cc_final: 0.8394 (mtt) REVERT: B 171 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8427 (ttp80) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.7216 time to fit residues: 63.9287 Evaluate side-chains 80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.107092 restraints weight = 18287.236| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.80 r_work: 0.2950 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7230 Z= 0.127 Angle : 0.517 6.548 9633 Z= 0.257 Chirality : 0.039 0.124 933 Planarity : 0.005 0.052 1155 Dihedral : 12.798 59.958 1314 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.36 % Allowed : 7.09 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.08 (0.30), residues: 771 helix: 2.53 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.91 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 171 TYR 0.014 0.001 TYR C 81 PHE 0.015 0.001 PHE C 134 TRP 0.016 0.002 TRP B 42 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7227) covalent geometry : angle 0.51705 / 0.26 ( 9633) hydrogen bonds : bond 0.04980 / 3.24 ( 438) hydrogen bonds : angle 3.91766 / 2.91 ( 1305) Misc. bond : bond 0.00062 / 0.03 ( 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 82 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.240 Fit side-chains REVERT: A 56 LYS cc_start: 0.8103 (tttp) cc_final: 0.7817 (tttt) REVERT: A 170 MET cc_start: 0.8659 (mtp) cc_final: 0.8400 (mtt) REVERT: A 174 LYS cc_start: 0.8406 (tttp) cc_final: 0.8188 (tmtp) REVERT: A 186 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6642 (tmm-80) REVERT: B 51 MET cc_start: 0.8630 (mtm) cc_final: 0.8415 (mtm) REVERT: B 170 MET cc_start: 0.8777 (mtm) cc_final: 0.8344 (mtt) REVERT: B 171 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8421 (ttp80) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.6757 time to fit residues: 57.0450 Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 33 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103587 restraints weight = 26268.911| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.31 r_work: 0.2735 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7230 Z= 0.199 Angle : 0.609 6.355 9633 Z= 0.305 Chirality : 0.043 0.130 933 Planarity : 0.005 0.034 1155 Dihedral : 13.764 59.848 1314 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.36 % Allowed : 7.39 % Favored : 91.25 % 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 (0.29), residues: 771 helix: 2.20 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.73 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.018 0.002 TYR C 81 PHE 0.018 0.002 PHE C 134 TRP 0.016 0.002 TRP B 42 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 7227) covalent geometry : angle 0.60940 / 0.30 ( 9633) hydrogen bonds : bond 0.06506 / 4.25 ( 438) hydrogen bonds : angle 4.19746 / 3.11 ( 1305) Misc. bond : bond 0.00126 / 0.06 ( 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 79 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.240 Fit side-chains REVERT: A 56 LYS cc_start: 0.8059 (tttp) cc_final: 0.7736 (tttt) REVERT: A 174 LYS cc_start: 0.8313 (tttp) cc_final: 0.7867 (ttpt) REVERT: A 186 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6538 (tmm-80) REVERT: B 170 MET cc_start: 0.8668 (mtm) cc_final: 0.8199 (mtt) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.7003 time to fit residues: 56.9510 Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 33 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101891 restraints weight = 23868.956| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.93 r_work: 0.2901 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7230 Z= 0.155 Angle : 0.552 6.251 9633 Z= 0.276 Chirality : 0.040 0.126 933 Planarity : 0.005 0.034 1155 Dihedral : 13.072 59.887 1314 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.36 % Allowed : 7.39 % Favored : 91.25 % 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: 2.77 (0.29), residues: 771 helix: 2.32 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.75 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 171 TYR 0.016 0.001 TYR A 81 PHE 0.017 0.002 PHE C 134 TRP 0.015 0.002 TRP A 42 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7227) covalent geometry : angle 0.55154 / 0.28 ( 9633) hydrogen bonds : bond 0.05654 / 3.68 ( 438) hydrogen bonds : angle 4.06059 / 3.01 ( 1305) Misc. bond : bond 0.00089 / 0.04 ( 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 79 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.257 Fit side-chains REVERT: A 56 LYS cc_start: 0.8105 (tttp) cc_final: 0.7824 (tttt) REVERT: A 174 LYS cc_start: 0.8400 (tttp) cc_final: 0.8171 (tmtp) REVERT: A 186 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6571 (tmm-80) REVERT: B 51 MET cc_start: 0.8595 (mtm) cc_final: 0.8361 (mtm) REVERT: B 170 MET cc_start: 0.8642 (mtm) cc_final: 0.8158 (mtt) outliers start: 6 outliers final: 5 residues processed: 78 average time/residue: 0.7350 time to fit residues: 59.8379 Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.102392 restraints weight = 19354.609| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.86 r_work: 0.2937 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7230 Z= 0.135 Angle : 0.524 6.079 9633 Z= 0.262 Chirality : 0.039 0.123 933 Planarity : 0.005 0.032 1155 Dihedral : 12.249 59.995 1314 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.36 % Allowed : 7.39 % Favored : 91.25 % 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: 2.94 (0.30), residues: 771 helix: 2.45 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.78 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.015 0.001 TYR C 81 PHE 0.015 0.001 PHE C 134 TRP 0.015 0.002 TRP A 42 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 7227) covalent geometry : angle 0.52403 / 0.26 ( 9633) hydrogen bonds : bond 0.05191 / 3.38 ( 438) hydrogen bonds : angle 3.97047 / 2.95 ( 1305) Misc. bond : bond 0.00068 / 0.03 ( 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 79 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.251 Fit side-chains REVERT: A 56 LYS cc_start: 0.8083 (tttp) cc_final: 0.7798 (tttt) REVERT: A 170 MET cc_start: 0.8642 (mtp) cc_final: 0.8376 (mtt) REVERT: A 174 LYS cc_start: 0.8404 (tttp) cc_final: 0.8187 (tmtp) REVERT: A 186 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6656 (tmm-80) REVERT: B 51 MET cc_start: 0.8633 (mtm) cc_final: 0.8417 (mtm) REVERT: B 170 MET cc_start: 0.8737 (mtm) cc_final: 0.8286 (mtt) outliers start: 6 outliers final: 5 residues processed: 78 average time/residue: 0.7741 time to fit residues: 62.9220 Evaluate side-chains 77 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 67 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107846 restraints weight = 28494.324| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.14 r_work: 0.2868 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7230 Z= 0.111 Angle : 0.489 5.894 9633 Z= 0.244 Chirality : 0.038 0.119 933 Planarity : 0.005 0.031 1155 Dihedral : 11.555 59.791 1314 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.21 % Allowed : 7.54 % Favored : 91.25 % 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: 3.18 (0.30), residues: 771 helix: 2.63 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.87 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.011 0.001 TYR C 81 PHE 0.015 0.001 PHE C 134 TRP 0.018 0.001 TRP A 42 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 7227) covalent geometry : angle 0.48865 / 0.24 ( 9633) hydrogen bonds : bond 0.04505 / 2.93 ( 438) hydrogen bonds : angle 3.84867 / 2.87 ( 1305) Misc. bond : bond 0.00036 / 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 78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.249 Fit side-chains REVERT: A 56 LYS cc_start: 0.8095 (tttp) cc_final: 0.7849 (tttt) REVERT: A 170 MET cc_start: 0.8435 (mtp) cc_final: 0.8173 (mtt) REVERT: A 174 LYS cc_start: 0.8289 (tttp) cc_final: 0.8059 (tmtp) REVERT: A 186 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6522 (tmm-80) REVERT: B 170 MET cc_start: 0.8666 (mtm) cc_final: 0.8190 (mtt) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.8265 time to fit residues: 67.0660 Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 33 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.138597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107839 restraints weight = 23522.291| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.07 r_work: 0.2946 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7230 Z= 0.110 Angle : 0.488 6.228 9633 Z= 0.243 Chirality : 0.037 0.121 933 Planarity : 0.005 0.031 1155 Dihedral : 11.123 59.862 1314 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.36 % Allowed : 7.69 % Favored : 90.95 % 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: 3.27 (0.30), residues: 771 helix: 2.68 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.95 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.011 0.001 TYR C 81 PHE 0.014 0.001 PHE C 134 TRP 0.017 0.001 TRP A 42 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 7227) covalent geometry : angle 0.48849 / 0.24 ( 9633) hydrogen bonds : bond 0.04431 / 2.89 ( 438) hydrogen bonds : angle 3.83201 / 2.86 ( 1305) Misc. bond : bond 0.00035 / 0.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.90 seconds wall clock time: 43 minutes 5.01 seconds (2585.01 seconds total)