Starting phenix.real_space_refine on Sat May 10 07:41:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4f_44179/05_2025/9b4f_44179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4f_44179/05_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_44179/05_2025/9b4f_44179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4f_44179/05_2025/9b4f_44179.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4f_44179/05_2025/9b4f_44179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4f_44179/05_2025/9b4f_44179.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.90, per 1000 atoms: 0.87 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: 1.41 Conformation dependent library (CDL) restraints added in 647.4 milliseconds 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: 0.53 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: 1.43 Time building geometry restraints manager: 1.64 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: 0.03 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: 2.200 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.360 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP A 176 HIS 0.002 0.001 HIS B 164 PHE 0.016 0.001 PHE A 313 TYR 0.008 0.001 TYR B 111 ARG 0.001 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.09275 ( 347) hydrogen bonds : angle 5.42184 ( 1023) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.66843 ( 4) covalent geometry : bond 0.00309 ( 5814) covalent geometry : angle 0.56920 ( 7930) *********************** 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 : 0.535 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: 0.2120 time to fit residues: 17.0054 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 : 0.757 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.178778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129706 restraints weight = 5809.470| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.21 r_work: 0.3256 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5816 Z= 0.106 Angle : 0.475 6.663 7934 Z= 0.252 Chirality : 0.037 0.116 868 Planarity : 0.004 0.038 946 Dihedral : 7.312 57.933 746 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.52 % Allowed : 8.89 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.34), residues: 662 helix: 0.89 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -3.47 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 176 HIS 0.002 0.000 HIS B 97 PHE 0.012 0.001 PHE A 313 TYR 0.013 0.001 TYR A 55 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 347) hydrogen bonds : angle 4.21655 ( 1023) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.29398 ( 4) covalent geometry : bond 0.00233 ( 5814) covalent geometry : angle 0.47463 ( 7930) *********************** 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 61 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.557 Fit side-chains REVERT: A 88 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: A 95 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.5049 (mpp80) REVERT: A 243 ARG cc_start: 0.7655 (mtp180) cc_final: 0.5845 (mmt180) REVERT: B 88 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7551 (m-10) REVERT: B 95 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.5011 (mpp80) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 0.1902 time to fit residues: 14.7746 Evaluate side-chains 51 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 51 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS B 125 GLN B 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.181137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133322 restraints weight = 5818.774| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.17 r_work: 0.3288 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5816 Z= 0.091 Angle : 0.441 7.212 7934 Z= 0.230 Chirality : 0.035 0.104 868 Planarity : 0.004 0.041 946 Dihedral : 6.508 57.378 742 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.18 % Allowed : 11.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.35), residues: 662 helix: 1.44 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -3.33 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.002 0.000 HIS B 164 PHE 0.010 0.001 PHE A 313 TYR 0.015 0.001 TYR B 55 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 347) hydrogen bonds : angle 3.90478 ( 1023) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.25726 ( 4) covalent geometry : bond 0.00195 ( 5814) covalent geometry : angle 0.44145 ( 7930) *********************** 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 63 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.604 Fit side-chains REVERT: A 95 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.5227 (mpp80) REVERT: A 172 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.7003 (t70) REVERT: A 243 ARG cc_start: 0.7618 (mtp180) cc_final: 0.5847 (mmt180) REVERT: B 95 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.5222 (mpp80) REVERT: B 172 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6977 (t70) outliers start: 13 outliers final: 3 residues processed: 57 average time/residue: 0.1842 time to fit residues: 14.0917 Evaluate side-chains 50 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS 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 55 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.186974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142852 restraints weight = 5918.982| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.08 r_work: 0.3281 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1455 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= 0.110 Angle : 0.459 7.627 7934 Z= 0.239 Chirality : 0.036 0.110 868 Planarity : 0.004 0.043 946 Dihedral : 6.078 59.769 736 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.02 % Allowed : 11.58 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.35), residues: 662 helix: 1.58 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -3.13 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.001 0.000 HIS B 164 PHE 0.011 0.001 PHE B 313 TYR 0.015 0.001 TYR A 55 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 347) hydrogen bonds : angle 3.88617 ( 1023) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.34224 ( 4) covalent geometry : bond 0.00252 ( 5814) covalent geometry : angle 0.45933 ( 7930) *********************** 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 64 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.589 Fit side-chains REVERT: A 88 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: A 95 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.5277 (mpp80) REVERT: A 172 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.7064 (t70) REVERT: A 243 ARG cc_start: 0.7681 (mtp180) cc_final: 0.5931 (mmt180) REVERT: B 95 ARG cc_start: 0.7043 (tmm-80) cc_final: 0.5244 (mpp80) REVERT: B 172 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.7034 (t70) outliers start: 18 outliers final: 9 residues processed: 59 average time/residue: 0.1777 time to fit residues: 14.3690 Evaluate side-chains 54 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.182726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135188 restraints weight = 5881.507| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.20 r_work: 0.3273 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1575 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= 0.105 Angle : 0.456 8.546 7934 Z= 0.235 Chirality : 0.036 0.109 868 Planarity : 0.004 0.043 946 Dihedral : 5.581 57.596 732 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.85 % Allowed : 12.42 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.35), residues: 662 helix: 1.72 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.08 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.001 0.000 HIS A 317 PHE 0.011 0.001 PHE A 313 TYR 0.015 0.001 TYR A 55 ARG 0.001 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 347) hydrogen bonds : angle 3.84845 ( 1023) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.32115 ( 4) covalent geometry : bond 0.00238 ( 5814) covalent geometry : angle 0.45578 ( 7930) *********************** 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 60 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.655 Fit side-chains REVERT: A 88 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7509 (m-10) REVERT: A 95 ARG cc_start: 0.6891 (tmm-80) cc_final: 0.5271 (mpp80) REVERT: A 172 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6922 (t70) REVERT: A 243 ARG cc_start: 0.7698 (mtp180) cc_final: 0.5911 (mmt180) REVERT: B 95 ARG cc_start: 0.6994 (tmm-80) cc_final: 0.5249 (mpp80) REVERT: B 172 HIS cc_start: 0.7129 (OUTLIER) cc_final: 0.6903 (t70) outliers start: 17 outliers final: 10 residues processed: 56 average time/residue: 0.1654 time to fit residues: 12.7409 Evaluate side-chains 52 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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 97 HIS 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 11 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.177570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129095 restraints weight = 5934.692| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.26 r_work: 0.3263 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1650 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= 0.109 Angle : 0.468 9.067 7934 Z= 0.237 Chirality : 0.036 0.108 868 Planarity : 0.004 0.043 946 Dihedral : 5.101 54.980 728 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.69 % Allowed : 12.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.35), residues: 662 helix: 1.73 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -3.01 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.001 0.000 HIS A 317 PHE 0.011 0.001 PHE B 313 TYR 0.015 0.001 TYR B 55 ARG 0.001 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 347) hydrogen bonds : angle 3.84509 ( 1023) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.32769 ( 4) covalent geometry : bond 0.00250 ( 5814) covalent geometry : angle 0.46768 ( 7930) *********************** 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 64 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.610 Fit side-chains REVERT: A 88 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7593 (m-10) REVERT: A 95 ARG cc_start: 0.6792 (tmm-80) cc_final: 0.5135 (mpp80) REVERT: A 172 HIS cc_start: 0.7232 (OUTLIER) cc_final: 0.6968 (t70) REVERT: A 243 ARG cc_start: 0.7741 (mtp180) cc_final: 0.5954 (mmt180) REVERT: B 88 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7337 (m-10) REVERT: B 95 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.5304 (mpp80) REVERT: B 172 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6995 (t70) outliers start: 22 outliers final: 9 residues processed: 57 average time/residue: 0.1649 time to fit residues: 12.9991 Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.177241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128901 restraints weight = 6006.195| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.24 r_work: 0.3254 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1716 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= 0.117 Angle : 0.476 9.326 7934 Z= 0.241 Chirality : 0.036 0.109 868 Planarity : 0.004 0.043 946 Dihedral : 5.056 52.313 728 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.19 % Allowed : 13.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.35), residues: 662 helix: 1.77 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.07 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.001 0.000 HIS A 317 PHE 0.011 0.001 PHE A 313 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 347) hydrogen bonds : angle 3.85123 ( 1023) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.34557 ( 4) covalent geometry : bond 0.00272 ( 5814) covalent geometry : angle 0.47622 ( 7930) *********************** 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 59 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.601 Fit side-chains REVERT: A 88 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7556 (m-10) REVERT: A 95 ARG cc_start: 0.6862 (tmm-80) cc_final: 0.5191 (mpp80) REVERT: A 172 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6891 (t70) REVERT: A 243 ARG cc_start: 0.7722 (mtp180) cc_final: 0.5915 (mmt180) REVERT: B 88 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: B 95 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.5297 (mpp80) REVERT: B 172 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6894 (t70) outliers start: 19 outliers final: 9 residues processed: 54 average time/residue: 0.1879 time to fit residues: 14.1124 Evaluate side-chains 54 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 97 HIS 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 B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 97 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.182954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.135724 restraints weight = 5833.637| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.20 r_work: 0.3263 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1800 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= 0.112 Angle : 0.477 9.701 7934 Z= 0.240 Chirality : 0.036 0.108 868 Planarity : 0.004 0.043 946 Dihedral : 4.927 49.840 728 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.19 % Allowed : 14.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.35), residues: 662 helix: 1.83 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.06 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 321 HIS 0.001 0.000 HIS A 41 PHE 0.011 0.001 PHE A 313 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 347) hydrogen bonds : angle 3.82816 ( 1023) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.33541 ( 4) covalent geometry : bond 0.00260 ( 5814) covalent geometry : angle 0.47715 ( 7930) *********************** 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 57 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.654 Fit side-chains REVERT: A 88 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7543 (m-10) REVERT: A 95 ARG cc_start: 0.6807 (tmm-80) cc_final: 0.5151 (mpp80) REVERT: A 172 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.6883 (t70) REVERT: A 243 ARG cc_start: 0.7722 (mtp180) cc_final: 0.5915 (mmt180) REVERT: B 88 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: B 95 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.5299 (mpp80) REVERT: B 172 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.6890 (t70) outliers start: 19 outliers final: 13 residues processed: 53 average time/residue: 0.1820 time to fit residues: 13.2212 Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 97 HIS 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 97 HIS 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 226 ASN 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 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 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 = 0.3923 r_free = 0.3923 target = 0.176198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128691 restraints weight = 5942.937| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.18 r_work: 0.3250 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1805 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 : 0.492 10.139 7934 Z= 0.247 Chirality : 0.037 0.110 868 Planarity : 0.004 0.043 946 Dihedral : 4.896 47.494 728 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.85 % Allowed : 14.93 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.35), residues: 662 helix: 1.79 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.06 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.001 0.000 HIS A 317 PHE 0.011 0.001 PHE A 313 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 347) hydrogen bonds : angle 3.86461 ( 1023) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.36340 ( 4) covalent geometry : bond 0.00291 ( 5814) covalent geometry : angle 0.49181 ( 7930) *********************** 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 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.591 Fit side-chains REVERT: A 88 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7666 (m-10) REVERT: A 95 ARG cc_start: 0.6863 (tmm-80) cc_final: 0.5196 (mpp80) REVERT: A 172 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6987 (t70) REVERT: A 243 ARG cc_start: 0.7762 (mtp180) cc_final: 0.6037 (mmt180) REVERT: B 88 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: B 95 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.5388 (mpp80) REVERT: B 172 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6993 (t70) outliers start: 17 outliers final: 12 residues processed: 52 average time/residue: 0.1740 time to fit residues: 12.3873 Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 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 47 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.0000 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.182607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134637 restraints weight = 5963.808| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.23 r_work: 0.3261 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1866 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= 0.107 Angle : 0.479 10.230 7934 Z= 0.239 Chirality : 0.036 0.108 868 Planarity : 0.004 0.043 946 Dihedral : 4.720 45.097 728 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.02 % Allowed : 14.77 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.35), residues: 662 helix: 1.89 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.03 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 321 HIS 0.001 0.000 HIS A 41 PHE 0.010 0.001 PHE A 313 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 347) hydrogen bonds : angle 3.80413 ( 1023) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.33215 ( 4) covalent geometry : bond 0.00244 ( 5814) covalent geometry : angle 0.47877 ( 7930) ********************** 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 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.563 Fit side-chains REVERT: A 88 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: A 95 ARG cc_start: 0.6789 (tmm-80) cc_final: 0.5144 (mpp80) REVERT: A 172 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6732 (t70) REVERT: A 243 ARG cc_start: 0.7737 (mtp180) cc_final: 0.5925 (mmt180) REVERT: B 88 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: B 95 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.5315 (mpp80) REVERT: B 172 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.6803 (t70) outliers start: 18 outliers final: 13 residues processed: 53 average time/residue: 0.1648 time to fit residues: 11.9364 Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 97 HIS 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 97 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 0.0000 chunk 50 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.179184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131133 restraints weight = 5908.248| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.23 r_work: 0.3274 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1975 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= 0.097 Angle : 0.469 10.362 7934 Z= 0.233 Chirality : 0.036 0.106 868 Planarity : 0.004 0.042 946 Dihedral : 4.487 40.508 728 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.52 % Allowed : 15.27 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.36), residues: 662 helix: 1.98 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.00 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 321 HIS 0.001 0.000 HIS A 41 PHE 0.010 0.001 PHE A 170 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 347) hydrogen bonds : angle 3.72194 ( 1023) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.34888 ( 4) covalent geometry : bond 0.00218 ( 5814) covalent geometry : angle 0.46865 ( 7930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.33 seconds wall clock time: 49 minutes 1.14 seconds (2941.14 seconds total)