Starting phenix.real_space_refine on Wed Sep 17 05:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4f_44179/09_2025/9b4f_44179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4f_44179/09_2025/9b4f_44179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b4f_44179/09_2025/9b4f_44179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4f_44179/09_2025/9b4f_44179.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4f_44179/09_2025/9b4f_44179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4f_44179/09_2025/9b4f_44179.cif" } resolution = 3.27 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= 0.001 sd= 0.023 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 Ca 2 9.91 5 S 40 5.16 5 C 3802 2.51 5 N 876 2.21 5 O 892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5612 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 9, 'TRANS': 325} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 1.97, per 1000 atoms: 0.35 Number of scatterers: 5612 At special positions: 0 Unit cell: (64.206, 127.674, 72.324, 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) Ca 2 19.99 S 40 16.00 O 892 8.00 N 876 7.00 C 3802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 213 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 213.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.544A pdb=" N ARG A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 87 Processing helix chain 'A' and resid 99 through 119 removed outlier: 3.944A pdb=" N PHE A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.046A pdb=" N ILE A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 162 " --> pdb=" O TRP A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 167 through 184 Processing helix chain 'A' and resid 185 through 203 removed outlier: 3.573A pdb=" N CYS A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.569A pdb=" N VAL A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 285 through 311 removed outlier: 3.876A pdb=" N TYR A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 342 removed outlier: 3.815A pdb=" N TRP A 321 " --> pdb=" O HIS A 317 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.936A pdb=" N ARG A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 373 removed outlier: 4.061A pdb=" N TRP A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.540A pdb=" N THR A 379 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 60 removed outlier: 3.544A pdb=" N ARG B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.944A pdb=" N PHE B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 157 through 162 removed outlier: 4.045A pdb=" N ILE B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 162 " --> pdb=" O TRP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 162' Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.573A pdb=" N CYS B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.570A pdb=" N VAL B 218 " --> pdb=" O TRP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 285 through 311 removed outlier: 3.876A pdb=" N TYR B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 342 removed outlier: 3.815A pdb=" N TRP B 321 " --> pdb=" O HIS B 317 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.936A pdb=" N ARG B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 373 removed outlier: 4.061A pdb=" N TRP B 355 " --> pdb=" O GLY B 351 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.539A pdb=" N THR B 379 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 409 347 hydrogen bonds defined for protein. 1023 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: 0.74 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1258 1.33 - 1.45: 1497 1.45 - 1.57: 2999 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 5814 Sorted by residual: bond pdb=" C ARG A 95 " pdb=" O ARG A 95 " ideal model delta sigma weight residual 1.238 1.215 0.023 1.28e-02 6.10e+03 3.21e+00 bond pdb=" C ARG B 95 " pdb=" O ARG B 95 " ideal model delta sigma weight residual 1.238 1.215 0.023 1.28e-02 6.10e+03 3.21e+00 bond pdb=" CA ARG A 95 " pdb=" C ARG A 95 " ideal model delta sigma weight residual 1.524 1.501 0.022 1.26e-02 6.30e+03 3.16e+00 bond pdb=" CA ARG B 95 " pdb=" C ARG B 95 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.26e-02 6.30e+03 3.05e+00 bond pdb=" C ALA A 332 " pdb=" N PRO A 333 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.24e-02 6.50e+03 1.39e+00 ... (remaining 5809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 7769 1.77 - 3.53: 141 3.53 - 5.30: 14 5.30 - 7.06: 4 7.06 - 8.83: 2 Bond angle restraints: 7930 Sorted by residual: angle pdb=" N GLU A 241 " pdb=" CA GLU A 241 " pdb=" C GLU A 241 " ideal model delta sigma weight residual 108.58 117.41 -8.83 1.82e+00 3.02e-01 2.35e+01 angle pdb=" N GLU B 241 " pdb=" CA GLU B 241 " pdb=" C GLU B 241 " ideal model delta sigma weight residual 108.58 117.39 -8.81 1.82e+00 3.02e-01 2.34e+01 angle pdb=" N ASP B 344 " pdb=" CA ASP B 344 " pdb=" C ASP B 344 " ideal model delta sigma weight residual 114.75 109.57 5.18 1.26e+00 6.30e-01 1.69e+01 angle pdb=" N ASP A 344 " pdb=" CA ASP A 344 " pdb=" C ASP A 344 " ideal model delta sigma weight residual 114.75 109.59 5.16 1.26e+00 6.30e-01 1.68e+01 angle pdb=" N HIS B 164 " pdb=" CA HIS B 164 " pdb=" C HIS B 164 " ideal model delta sigma weight residual 114.56 110.39 4.17 1.27e+00 6.20e-01 1.08e+01 ... (remaining 7925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 2906 14.82 - 29.64: 228 29.64 - 44.47: 62 44.47 - 59.29: 10 59.29 - 74.11: 6 Dihedral angle restraints: 3212 sinusoidal: 1252 harmonic: 1960 Sorted by residual: dihedral pdb=" C ARG A 95 " pdb=" N ARG A 95 " pdb=" CA ARG A 95 " pdb=" CB ARG A 95 " ideal model delta harmonic sigma weight residual -122.60 -134.78 12.18 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" C ARG B 95 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " pdb=" CB ARG B 95 " ideal model delta harmonic sigma weight residual -122.60 -134.75 12.15 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" N ARG A 95 " pdb=" C ARG A 95 " pdb=" CA ARG A 95 " pdb=" CB ARG A 95 " ideal model delta harmonic sigma weight residual 122.80 132.58 -9.78 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 3209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 862 0.102 - 0.203: 4 0.203 - 0.305: 0 0.305 - 0.406: 0 0.406 - 0.508: 2 Chirality restraints: 868 Sorted by residual: chirality pdb=" CA ARG A 95 " pdb=" N ARG A 95 " pdb=" C ARG A 95 " pdb=" CB ARG A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA ARG B 95 " pdb=" N ARG B 95 " pdb=" C ARG B 95 " pdb=" CB ARG B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CA GLU A 241 " pdb=" N GLU A 241 " pdb=" C GLU A 241 " pdb=" CB GLU A 241 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 865 not shown) Planarity restraints: 946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 97 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 98 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 97 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO B 98 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 220 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C LEU B 220 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU B 220 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP B 221 " -0.009 2.00e-02 2.50e+03 ... (remaining 943 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1377 2.78 - 3.31: 5355 3.31 - 3.84: 9065 3.84 - 4.37: 9926 4.37 - 4.90: 18231 Nonbonded interactions: 43954 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" O ARG A 102 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 84 " pdb=" O ARG B 102 " model vdw 2.256 3.040 nonbonded pdb=" O ILE B 327 " pdb=" OG1 THR B 331 " model vdw 2.275 3.040 nonbonded pdb=" O ILE A 327 " pdb=" OG1 THR A 331 " model vdw 2.275 3.040 nonbonded pdb=" NH1 ARG B 95 " pdb=" O GLU B 241 " model vdw 2.302 3.120 ... (remaining 43949 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5816 Z= 0.153 Angle : 0.569 8.829 7934 Z= 0.352 Chirality : 0.043 0.508 868 Planarity : 0.004 0.043 946 Dihedral : 12.087 74.110 1942 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.68 % Allowed : 6.04 % Favored : 92.28 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.30), residues: 662 helix: -0.36 (0.22), residues: 478 sheet: None (None), residues: 0 loop : -4.04 (0.37), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.008 0.001 TYR B 111 PHE 0.016 0.001 PHE A 313 TRP 0.011 0.001 TRP A 176 HIS 0.002 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5814) covalent geometry : angle 0.56920 ( 7930) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.66843 ( 4) hydrogen bonds : bond 0.09275 ( 347) hydrogen bonds : angle 5.42184 ( 1023) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.228 Fit side-chains REVERT: A 88 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: A 95 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.5737 (mpp80) REVERT: A 243 ARG cc_start: 0.7602 (mtp180) cc_final: 0.6434 (mmt180) REVERT: B 95 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.5652 (mpp80) REVERT: B 243 ARG cc_start: 0.7579 (mtp180) cc_final: 0.6371 (mmt180) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.0943 time to fit residues: 7.5721 Evaluate side-chains 53 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 309 HIS B 41 HIS B 97 HIS B 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.178397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129081 restraints weight = 5884.301| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.23 r_work: 0.3247 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5816 Z= 0.110 Angle : 0.478 6.629 7934 Z= 0.253 Chirality : 0.037 0.121 868 Planarity : 0.004 0.038 946 Dihedral : 7.277 59.979 746 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.52 % Allowed : 8.72 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.34), residues: 662 helix: 0.89 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -3.45 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.015 0.001 TYR B 55 PHE 0.013 0.001 PHE B 313 TRP 0.013 0.001 TRP A 176 HIS 0.002 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 5814) covalent geometry : angle 0.47803 ( 7930) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.30694 ( 4) hydrogen bonds : bond 0.03272 ( 347) hydrogen bonds : angle 4.21990 ( 1023) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.207 Fit side-chains REVERT: A 88 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7290 (m-10) REVERT: A 95 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.5149 (mpp80) REVERT: A 243 ARG cc_start: 0.7664 (mtp180) cc_final: 0.5847 (mmt180) REVERT: B 88 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7571 (m-10) REVERT: B 95 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5061 (mpp80) outliers start: 15 outliers final: 6 residues processed: 59 average time/residue: 0.0833 time to fit residues: 6.5093 Evaluate side-chains 52 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.173503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127662 restraints weight = 5865.813| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.07 r_work: 0.3249 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5816 Z= 0.126 Angle : 0.478 7.259 7934 Z= 0.249 Chirality : 0.037 0.111 868 Planarity : 0.004 0.043 946 Dihedral : 6.778 56.896 742 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.68 % Allowed : 10.57 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.35), residues: 662 helix: 1.19 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -3.41 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.015 0.001 TYR B 55 PHE 0.012 0.001 PHE B 313 TRP 0.014 0.001 TRP A 176 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5814) covalent geometry : angle 0.47768 ( 7930) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.30055 ( 4) hydrogen bonds : bond 0.03499 ( 347) hydrogen bonds : angle 4.07416 ( 1023) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.203 Fit side-chains REVERT: A 88 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: A 95 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.5277 (mpp80) REVERT: A 243 ARG cc_start: 0.7666 (mtp180) cc_final: 0.5915 (mmt180) REVERT: B 88 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7610 (m-10) REVERT: B 95 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.5208 (mpp80) outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 0.0872 time to fit residues: 6.5966 Evaluate side-chains 53 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.190216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147028 restraints weight = 5817.564| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.04 r_work: 0.3259 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5816 Z= 0.131 Angle : 0.481 7.503 7934 Z= 0.251 Chirality : 0.037 0.112 868 Planarity : 0.004 0.043 946 Dihedral : 6.737 59.041 742 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.19 % Allowed : 11.07 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.35), residues: 662 helix: 1.56 (0.25), residues: 476 sheet: None (None), residues: 0 loop : -3.07 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.014 0.001 TYR A 55 PHE 0.013 0.001 PHE A 313 TRP 0.012 0.001 TRP A 174 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5814) covalent geometry : angle 0.48120 ( 7930) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.32725 ( 4) hydrogen bonds : bond 0.03522 ( 347) hydrogen bonds : angle 4.02615 ( 1023) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.209 Fit side-chains REVERT: A 88 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7743 (m-10) REVERT: A 95 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.5273 (mpp80) REVERT: A 243 ARG cc_start: 0.7775 (mtp180) cc_final: 0.5952 (mmt180) REVERT: B 88 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7783 (m-10) REVERT: B 95 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.5286 (mpp80) outliers start: 19 outliers final: 12 residues processed: 60 average time/residue: 0.0838 time to fit residues: 6.6754 Evaluate side-chains 57 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.175314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127144 restraints weight = 6060.798| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.23 r_work: 0.3218 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5816 Z= 0.148 Angle : 0.500 8.125 7934 Z= 0.258 Chirality : 0.038 0.114 868 Planarity : 0.004 0.045 946 Dihedral : 6.750 58.822 742 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.52 % Allowed : 12.58 % Favored : 83.89 % 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 aren not related in a simple way. whole: 0.40 (0.35), residues: 662 helix: 1.40 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -3.16 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.015 0.001 TYR B 55 PHE 0.013 0.001 PHE B 313 TRP 0.012 0.001 TRP B 174 HIS 0.001 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5814) covalent geometry : angle 0.49967 ( 7930) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.34218 ( 4) hydrogen bonds : bond 0.03721 ( 347) hydrogen bonds : angle 4.06620 ( 1023) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.200 Fit side-chains REVERT: A 88 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: A 95 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.5327 (mpp80) REVERT: A 172 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6905 (t70) REVERT: A 243 ARG cc_start: 0.7714 (mtp180) cc_final: 0.5914 (mmt180) REVERT: B 88 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7578 (m-10) REVERT: B 95 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.5283 (mpp80) outliers start: 21 outliers final: 10 residues processed: 58 average time/residue: 0.0750 time to fit residues: 5.9621 Evaluate side-chains 57 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.181826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.134935 restraints weight = 5894.313| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.18 r_work: 0.3241 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5816 Z= 0.124 Angle : 0.485 8.703 7934 Z= 0.248 Chirality : 0.037 0.110 868 Planarity : 0.004 0.045 946 Dihedral : 6.573 57.120 742 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.02 % Allowed : 13.09 % Favored : 83.89 % 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 aren not related in a simple way. whole: 0.64 (0.35), residues: 662 helix: 1.57 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.08 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 95 TYR 0.015 0.001 TYR A 55 PHE 0.013 0.001 PHE A 313 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5814) covalent geometry : angle 0.48514 ( 7930) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.32740 ( 4) hydrogen bonds : bond 0.03428 ( 347) hydrogen bonds : angle 3.99009 ( 1023) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.209 Fit side-chains REVERT: A 88 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7637 (m-10) REVERT: A 95 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5305 (mpp80) REVERT: A 172 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7138 (t70) REVERT: A 243 ARG cc_start: 0.7714 (mtp180) cc_final: 0.5999 (mmt180) REVERT: B 88 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: B 95 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.5344 (mpp80) REVERT: B 172 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.7142 (t70) outliers start: 18 outliers final: 9 residues processed: 55 average time/residue: 0.0784 time to fit residues: 5.8957 Evaluate side-chains 57 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.189044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144491 restraints weight = 5913.159| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.14 r_work: 0.3243 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5816 Z= 0.131 Angle : 0.494 9.143 7934 Z= 0.251 Chirality : 0.037 0.111 868 Planarity : 0.004 0.045 946 Dihedral : 6.401 55.102 740 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.85 % Allowed : 13.76 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.35), residues: 662 helix: 1.59 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -3.02 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 95 TYR 0.015 0.001 TYR B 55 PHE 0.012 0.001 PHE B 313 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5814) covalent geometry : angle 0.49381 ( 7930) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.33395 ( 4) hydrogen bonds : bond 0.03517 ( 347) hydrogen bonds : angle 3.97320 ( 1023) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.205 Fit side-chains REVERT: A 88 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7606 (m-10) REVERT: A 95 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.5354 (mpp80) REVERT: A 172 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7196 (t70) REVERT: A 243 ARG cc_start: 0.7716 (mtp180) cc_final: 0.6007 (mmt180) REVERT: B 88 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7651 (m-10) REVERT: B 95 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.5345 (mpp80) REVERT: B 172 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7182 (t70) outliers start: 17 outliers final: 11 residues processed: 53 average time/residue: 0.0776 time to fit residues: 5.6091 Evaluate side-chains 61 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.182337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135638 restraints weight = 5860.176| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.18 r_work: 0.3243 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5816 Z= 0.126 Angle : 0.494 9.595 7934 Z= 0.249 Chirality : 0.037 0.110 868 Planarity : 0.004 0.045 946 Dihedral : 6.183 52.945 738 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.36 % Allowed : 13.76 % Favored : 82.89 % 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 aren not related in a simple way. whole: 0.77 (0.35), residues: 662 helix: 1.65 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -2.98 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 95 TYR 0.015 0.001 TYR A 55 PHE 0.012 0.001 PHE A 313 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5814) covalent geometry : angle 0.49443 ( 7930) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.35373 ( 4) hydrogen bonds : bond 0.03435 ( 347) hydrogen bonds : angle 3.93861 ( 1023) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.205 Fit side-chains REVERT: A 88 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: A 95 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.5361 (mpp80) REVERT: A 172 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.7082 (t70) REVERT: A 243 ARG cc_start: 0.7681 (mtp180) cc_final: 0.5906 (mmt180) REVERT: B 88 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7573 (m-10) REVERT: B 95 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.5368 (mpp80) REVERT: B 172 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.7110 (t70) outliers start: 20 outliers final: 11 residues processed: 55 average time/residue: 0.0715 time to fit residues: 5.4249 Evaluate side-chains 57 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.189770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144760 restraints weight = 5819.724| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.16 r_work: 0.3259 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5816 Z= 0.109 Angle : 0.482 10.042 7934 Z= 0.241 Chirality : 0.036 0.108 868 Planarity : 0.004 0.045 946 Dihedral : 5.883 50.015 738 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.85 % Allowed : 14.26 % Favored : 82.89 % 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 aren not related in a simple way. whole: 0.93 (0.35), residues: 662 helix: 1.82 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.04 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 95 TYR 0.016 0.001 TYR A 55 PHE 0.011 0.001 PHE B 313 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5814) covalent geometry : angle 0.48248 ( 7930) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.35100 ( 4) hydrogen bonds : bond 0.03184 ( 347) hydrogen bonds : angle 3.84406 ( 1023) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.173 Fit side-chains REVERT: A 88 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7415 (m-10) REVERT: A 95 ARG cc_start: 0.6994 (tmm-80) cc_final: 0.5432 (mpp80) REVERT: A 172 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.7069 (t70) REVERT: A 243 ARG cc_start: 0.7722 (mtp180) cc_final: 0.5984 (mmt180) REVERT: B 88 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: B 172 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.7079 (t70) outliers start: 17 outliers final: 10 residues processed: 54 average time/residue: 0.0629 time to fit residues: 4.8091 Evaluate side-chains 53 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.0070 chunk 53 optimal weight: 0.1980 chunk 16 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.193907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148943 restraints weight = 5822.047| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.18 r_work: 0.3326 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5816 Z= 0.087 Angle : 0.479 10.186 7934 Z= 0.233 Chirality : 0.035 0.104 868 Planarity : 0.004 0.044 946 Dihedral : 4.865 45.052 730 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.01 % Allowed : 15.10 % Favored : 82.89 % 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 aren not related in a simple way. whole: 1.27 (0.36), residues: 662 helix: 2.11 (0.25), residues: 482 sheet: None (None), residues: 0 loop : -2.91 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 323 TYR 0.016 0.001 TYR A 55 PHE 0.010 0.001 PHE A 170 TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 5814) covalent geometry : angle 0.47914 ( 7930) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.34267 ( 4) hydrogen bonds : bond 0.02777 ( 347) hydrogen bonds : angle 3.69716 ( 1023) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.198 Fit side-chains REVERT: A 95 ARG cc_start: 0.6784 (tmm-80) cc_final: 0.5201 (mpp80) REVERT: A 172 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6691 (t70) REVERT: A 243 ARG cc_start: 0.7681 (mtp180) cc_final: 0.5891 (mmt180) REVERT: B 95 ARG cc_start: 0.6860 (tmm-80) cc_final: 0.5253 (mpp80) REVERT: B 172 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6712 (t70) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.0896 time to fit residues: 6.1914 Evaluate side-chains 50 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.192296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.148253 restraints weight = 5770.222| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.10 r_work: 0.3290 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5816 Z= 0.106 Angle : 0.495 10.171 7934 Z= 0.242 Chirality : 0.036 0.108 868 Planarity : 0.004 0.043 946 Dihedral : 4.584 42.864 728 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.68 % Allowed : 15.77 % Favored : 82.55 % 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 aren not related in a simple way. whole: 1.27 (0.36), residues: 662 helix: 2.07 (0.25), residues: 484 sheet: None (None), residues: 0 loop : -2.84 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 60 TYR 0.017 0.001 TYR B 55 PHE 0.010 0.001 PHE A 313 TRP 0.013 0.001 TRP B 321 HIS 0.001 0.000 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5814) covalent geometry : angle 0.49486 ( 7930) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.36764 ( 4) hydrogen bonds : bond 0.03107 ( 347) hydrogen bonds : angle 3.73383 ( 1023) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1411.45 seconds wall clock time: 24 minutes 54.50 seconds (1494.50 seconds total)