Starting phenix.real_space_refine on Thu Jul 2 06:48:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h86_34530/07_2026/8h86_34530.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h86_34530/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8h86_34530/07_2026/8h86_34530.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h86_34530/07_2026/8h86_34530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h86_34530/07_2026/8h86_34530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h86_34530/07_2026/8h86_34530.map" model { file = "/net/cci-nas-00/data/ceres_data/8h86_34530/07_2026/8h86_34530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h86_34530/07_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-dev-6108/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: 1.55, per 1000 atoms: 0.22 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: 0.46 Conformation dependent library (CDL) restraints added in 606.5 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: 0.14 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: 0.97 Time building geometry restraints manager: 0.63 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.270 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- 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 : 0.152 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: 0.5597 time to fit residues: 56.6993 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 : 0.235 ------------------------------------------------------------------------------- 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: 0.0970 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.133792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.105236 restraints weight = 14262.422| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.64 r_work: 0.2744 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 7230 Z= 0.321 Angle : 1.442 52.238 9633 Z= 0.673 Chirality : 0.069 0.516 933 Planarity : 0.015 0.192 1155 Dihedral : 20.377 119.221 1314 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Rotamer: Outliers : 1.81 % Allowed : 5.43 % Favored : 92.76 % Cbeta Deviations : 0.14 % 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: -0.22 (0.29), residues: 771 helix: 0.01 (0.20), residues: 540 sheet: None (None), residues: 0 loop : -0.16 (0.45), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.004 ARG C 128 TYR 0.159 0.008 TYR C 45 PHE 0.097 0.008 PHE C 131 TRP 0.076 0.007 TRP B 190 HIS 0.041 0.006 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.32 ( 7227) covalent geometry : angle 1.44219 / 0.67 ( 9633) hydrogen bonds : bond 0.09953 / 6.61 ( 438) hydrogen bonds : angle 5.64682 / 4.12 ( 1305) Misc. bond : bond 0.00111 / 0.06 ( 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 95 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.235 Fit side-chains REVERT: A 20 MET cc_start: 0.8722 (mtm) cc_final: 0.8512 (mtm) REVERT: A 170 MET cc_start: 0.8501 (mtm) cc_final: 0.8270 (mtt) REVERT: A 174 LYS cc_start: 0.8283 (tttp) cc_final: 0.7768 (mtmt) REVERT: B 60 SER cc_start: 0.8690 (m) cc_final: 0.8423 (t) REVERT: B 87 ASP cc_start: 0.9114 (t70) cc_final: 0.8818 (t70) REVERT: B 170 MET cc_start: 0.8647 (mtm) cc_final: 0.8307 (mtt) REVERT: B 174 LYS cc_start: 0.8252 (tttt) cc_final: 0.7652 (mtmt) outliers start: 9 outliers final: 1 residues processed: 90 average time/residue: 0.5319 time to fit residues: 50.1367 Evaluate side-chains 81 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105737 restraints weight = 22857.823| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.04 r_work: 0.2722 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7230 Z= 0.160 Angle : 0.605 7.562 9633 Z= 0.302 Chirality : 0.042 0.131 933 Planarity : 0.005 0.036 1155 Dihedral : 17.915 85.722 1314 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.06 % Allowed : 6.49 % 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: 2.31 (0.30), residues: 771 helix: 1.88 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.85 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 171 TYR 0.015 0.002 TYR C 81 PHE 0.024 0.002 PHE C 221 TRP 0.023 0.002 TRP B 42 HIS 0.005 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 7227) covalent geometry : angle 0.60479 / 0.30 ( 9633) hydrogen bonds : bond 0.05832 / 3.80 ( 438) hydrogen bonds : angle 4.26469 / 3.17 ( 1305) Misc. bond : bond 0.00082 / 0.04 ( 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 83 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.162 Fit side-chains REVERT: A 56 LYS cc_start: 0.8002 (tttp) cc_final: 0.7742 (tttt) REVERT: A 62 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8154 (mtt180) REVERT: B 170 MET cc_start: 0.8778 (mtm) cc_final: 0.8345 (mtt) outliers start: 4 outliers final: 2 residues processed: 81 average time/residue: 0.5084 time to fit residues: 43.1758 Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS 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: 9.9990 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 overall best weight: 2.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN C 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103548 restraints weight = 20900.507| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.97 r_work: 0.2894 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2249 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= 0.155 Angle : 0.575 6.304 9633 Z= 0.288 Chirality : 0.041 0.128 933 Planarity : 0.005 0.033 1155 Dihedral : 15.641 63.548 1314 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.66 % Allowed : 7.09 % 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: 2.71 (0.30), residues: 771 helix: 2.21 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 171 TYR 0.015 0.002 TYR C 81 PHE 0.020 0.002 PHE C 221 TRP 0.022 0.002 TRP B 42 HIS 0.004 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7227) covalent geometry : angle 0.57496 / 0.29 ( 9633) hydrogen bonds : bond 0.05835 / 3.81 ( 438) hydrogen bonds : angle 4.14221 / 3.08 ( 1305) Misc. bond : bond 0.00081 / 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 83 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.202 Fit side-chains REVERT: A 56 LYS cc_start: 0.8076 (tttp) cc_final: 0.7808 (tttt) REVERT: A 170 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8328 (mtt) REVERT: A 174 LYS cc_start: 0.8437 (tttp) cc_final: 0.7986 (ttpt) REVERT: B 170 MET cc_start: 0.8712 (mtm) cc_final: 0.8301 (mtt) REVERT: B 171 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8421 (ttp-170) outliers start: 8 outliers final: 2 residues processed: 78 average time/residue: 0.5683 time to fit residues: 46.3344 Evaluate side-chains 73 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain C residue 60 SER 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: 7.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.133735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.103417 restraints weight = 20100.953| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.98 r_work: 0.2920 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7230 Z= 0.211 Angle : 0.633 6.171 9633 Z= 0.318 Chirality : 0.045 0.131 933 Planarity : 0.005 0.043 1155 Dihedral : 15.522 63.517 1314 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.21 % Allowed : 7.39 % Favored : 91.40 % 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: 2.38 (0.29), residues: 771 helix: 1.98 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.72 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 171 TYR 0.018 0.002 TYR C 81 PHE 0.019 0.002 PHE B 134 TRP 0.020 0.002 TRP B 42 HIS 0.006 0.002 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 ( 7227) covalent geometry : angle 0.63266 / 0.32 ( 9633) hydrogen bonds : bond 0.06795 / 4.43 ( 438) hydrogen bonds : angle 4.28149 / 3.17 ( 1305) Misc. bond : bond 0.00133 / 0.07 ( 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 79 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.215 Fit side-chains REVERT: A 56 LYS cc_start: 0.7968 (tttp) cc_final: 0.7691 (tttt) REVERT: A 105 ASP cc_start: 0.8672 (p0) cc_final: 0.8450 (p0) REVERT: A 170 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8264 (mtt) REVERT: A 174 LYS cc_start: 0.8447 (tttp) cc_final: 0.7998 (ttpt) REVERT: B 170 MET cc_start: 0.8739 (mtm) cc_final: 0.8279 (mtt) REVERT: C 171 ARG cc_start: 0.8475 (ttp-170) cc_final: 0.8266 (ttp-170) outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.5771 time to fit residues: 46.4307 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 : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 60 SER 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: 1.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.132950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.101883 restraints weight = 18213.783| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.83 r_work: 0.2938 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2565 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= 0.126 Angle : 0.516 6.254 9633 Z= 0.257 Chirality : 0.039 0.123 933 Planarity : 0.005 0.035 1155 Dihedral : 13.487 59.689 1314 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 7.84 % Favored : 91.10 % 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: 2.92 (0.30), residues: 771 helix: 2.42 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.83 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 171 TYR 0.014 0.001 TYR C 81 PHE 0.016 0.001 PHE B 134 TRP 0.019 0.002 TRP B 42 HIS 0.003 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 7227) covalent geometry : angle 0.51568 / 0.26 ( 9633) hydrogen bonds : bond 0.04929 / 3.21 ( 438) hydrogen bonds : angle 3.93537 / 2.93 ( 1305) Misc. bond : bond 0.00060 / 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 78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.230 Fit side-chains REVERT: A 56 LYS cc_start: 0.8095 (tttp) cc_final: 0.7827 (tttt) REVERT: A 170 MET cc_start: 0.8562 (mtp) cc_final: 0.8277 (mtt) REVERT: B 170 MET cc_start: 0.8683 (mtm) cc_final: 0.8201 (mtt) REVERT: B 171 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8384 (ttp80) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.5845 time to fit residues: 46.9433 Evaluate side-chains 74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 51 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.141842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112822 restraints weight = 27591.574| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.12 r_work: 0.2808 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7230 Z= 0.109 Angle : 0.485 5.898 9633 Z= 0.242 Chirality : 0.037 0.121 933 Planarity : 0.005 0.032 1155 Dihedral : 12.034 59.969 1314 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.06 % Allowed : 7.69 % 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: 3.22 (0.30), residues: 771 helix: 2.66 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.89 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 171 TYR 0.012 0.001 TYR C 81 PHE 0.015 0.001 PHE B 134 TRP 0.018 0.001 TRP B 42 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 7227) covalent geometry : angle 0.48533 / 0.24 ( 9633) hydrogen bonds : bond 0.04381 / 2.85 ( 438) hydrogen bonds : angle 3.79708 / 2.83 ( 1305) Misc. bond : bond 0.00037 / 0.02 ( 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: 4 poor density : 75 time to evaluate : 0.234 Fit side-chains REVERT: A 56 LYS cc_start: 0.8143 (tttp) cc_final: 0.7872 (tttt) REVERT: A 170 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8225 (mtt) REVERT: A 248 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 170 MET cc_start: 0.8620 (mtm) cc_final: 0.8205 (mtt) REVERT: B 171 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8383 (ttp80) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.6439 time to fit residues: 51.6298 Evaluate side-chains 78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 174 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS B 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099100 restraints weight = 23442.250| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.99 r_work: 0.2856 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7230 Z= 0.210 Angle : 0.626 6.388 9633 Z= 0.314 Chirality : 0.045 0.130 933 Planarity : 0.005 0.041 1155 Dihedral : 13.417 59.316 1314 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.06 % Allowed : 8.60 % Favored : 90.35 % 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: 2.58 (0.29), residues: 771 helix: 2.16 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.71 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 171 TYR 0.018 0.002 TYR C 81 PHE 0.019 0.002 PHE B 134 TRP 0.017 0.002 TRP C 190 HIS 0.006 0.002 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 ( 7227) covalent geometry : angle 0.62577 / 0.31 ( 9633) hydrogen bonds : bond 0.06699 / 4.37 ( 438) hydrogen bonds : angle 4.21650 / 3.12 ( 1305) Misc. bond : bond 0.00135 / 0.07 ( 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 80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.158 Fit side-chains REVERT: A 56 LYS cc_start: 0.8188 (tttp) cc_final: 0.7887 (tttt) REVERT: A 170 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8234 (mtt) REVERT: A 174 LYS cc_start: 0.8507 (tmtp) cc_final: 0.8025 (ttpt) REVERT: B 170 MET cc_start: 0.8621 (mtm) cc_final: 0.8177 (mtt) outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 0.5847 time to fit residues: 47.7066 Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain B 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: 0.7980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.133358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102327 restraints weight = 19326.879| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.86 r_work: 0.2940 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7230 Z= 0.141 Angle : 0.536 6.172 9633 Z= 0.269 Chirality : 0.040 0.125 933 Planarity : 0.005 0.034 1155 Dihedral : 12.388 59.317 1314 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.21 % Allowed : 8.60 % Favored : 90.20 % 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: 2.81 (0.29), residues: 771 helix: 2.35 (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 0.003 0.000 ARG C 46 TYR 0.015 0.001 TYR C 45 PHE 0.017 0.001 PHE B 134 TRP 0.017 0.002 TRP A 42 HIS 0.003 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7227) covalent geometry : angle 0.53610 / 0.27 ( 9633) hydrogen bonds : bond 0.05348 / 3.48 ( 438) hydrogen bonds : angle 4.00900 / 2.97 ( 1305) Misc. bond : bond 0.00074 / 0.04 ( 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 78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.144 Fit side-chains REVERT: A 56 LYS cc_start: 0.8086 (tttp) cc_final: 0.7809 (tttt) REVERT: A 170 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8379 (mtt) REVERT: A 186 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6727 (tmm-80) REVERT: B 170 MET cc_start: 0.8734 (mtm) cc_final: 0.8241 (mtt) REVERT: B 176 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7626 (ttm-80) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.5528 time to fit residues: 43.8942 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B 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: 4.9990 chunk 4 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.135210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.104452 restraints weight = 27431.814| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.11 r_work: 0.2892 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7230 Z= 0.134 Angle : 0.528 6.051 9633 Z= 0.265 Chirality : 0.039 0.123 933 Planarity : 0.005 0.040 1155 Dihedral : 11.994 59.740 1314 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.21 % Allowed : 8.90 % Favored : 89.89 % 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: 2.89 (0.30), residues: 771 helix: 2.41 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.77 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 171 TYR 0.015 0.001 TYR C 45 PHE 0.016 0.001 PHE B 134 TRP 0.017 0.002 TRP B 42 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7227) covalent geometry : angle 0.52835 / 0.27 ( 9633) hydrogen bonds : bond 0.05206 / 3.39 ( 438) hydrogen bonds : angle 3.98862 / 2.96 ( 1305) Misc. bond : bond 0.00067 / 0.03 ( 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 79 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.167 Fit side-chains REVERT: A 56 LYS cc_start: 0.8136 (tttp) cc_final: 0.7882 (tttt) REVERT: A 170 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8218 (mtt) REVERT: A 186 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6598 (tmm-80) REVERT: B 170 MET cc_start: 0.8596 (mtm) cc_final: 0.8119 (mtt) REVERT: B 176 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7585 (ttm-80) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.6690 time to fit residues: 53.5952 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 : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain B 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 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.135689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104654 restraints weight = 23625.685| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.01 r_work: 0.2939 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2782 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= 0.118 Angle : 0.506 5.821 9633 Z= 0.254 Chirality : 0.038 0.121 933 Planarity : 0.005 0.033 1155 Dihedral : 11.416 59.408 1314 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.21 % Allowed : 8.90 % Favored : 89.89 % 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: 3.05 (0.30), residues: 771 helix: 2.53 (0.21), residues: 546 sheet: None (None), residues: 0 loop : 0.83 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 171 TYR 0.014 0.001 TYR C 45 PHE 0.015 0.001 PHE B 134 TRP 0.018 0.002 TRP B 42 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 7227) covalent geometry : angle 0.50586 / 0.25 ( 9633) hydrogen bonds : bond 0.04715 / 3.07 ( 438) hydrogen bonds : angle 3.90663 / 2.91 ( 1305) Misc. bond : bond 0.00046 / 0.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2015.75 seconds wall clock time: 35 minutes 4.77 seconds (2104.77 seconds total)