Starting phenix.real_space_refine on Tue Jan 14 04:23:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4f_44179/01_2025/9b4f_44179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4f_44179/01_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_44179/01_2025/9b4f_44179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4f_44179/01_2025/9b4f_44179.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4f_44179/01_2025/9b4f_44179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4f_44179/01_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-5571/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: 4.97, per 1000 atoms: 0.89 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 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: 1.45 Conformation dependent library (CDL) restraints added in 682.1 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: 0.47 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: 1.37 Time building geometry restraints manager: 1.65 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: 2905 14.82 - 29.64: 226 29.64 - 44.47: 62 44.47 - 59.29: 10 59.29 - 74.11: 6 Dihedral angle restraints: 3209 sinusoidal: 1249 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 3206 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: 2.03 - 2.61: 47 2.61 - 3.18: 4911 3.18 - 3.75: 8461 3.75 - 4.33: 11186 4.33 - 4.90: 19352 Nonbonded interactions: 43957 Sorted by model distance: nonbonded pdb=" SG CYS B 153 " pdb=" SG CYS B 213 " model vdw 2.032 3.760 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 ... (remaining 43952 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: 0.010 Normalize map: mean=0, sd=1: 2.070 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 17.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- 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 5814 Z= 0.198 Angle : 0.569 8.829 7930 Z= 0.352 Chirality : 0.043 0.508 868 Planarity : 0.004 0.043 946 Dihedral : 12.087 74.110 1942 Min Nonbonded Distance : 2.032 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 *********************** 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 : 0.544 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: 0.2123 time to fit residues: 17.0752 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 : 0.575 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.178168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129209 restraints weight = 5844.586| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.22 r_work: 0.3254 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5814 Z= 0.152 Angle : 0.477 6.662 7930 Z= 0.253 Chirality : 0.037 0.111 868 Planarity : 0.004 0.038 946 Dihedral : 7.200 58.612 746 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % 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 (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: -0.29 (0.34), residues: 662 helix: 0.96 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -3.43 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 176 HIS 0.002 0.001 HIS B 97 PHE 0.012 0.001 PHE B 313 TYR 0.015 0.001 TYR A 55 ARG 0.003 0.000 ARG B 286 *********************** 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 : 0.529 Fit side-chains REVERT: A 88 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7258 (m-10) REVERT: A 95 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.5097 (mpp80) REVERT: B 88 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7565 (m-10) REVERT: B 95 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.5145 (mpp80) outliers start: 15 outliers final: 6 residues processed: 59 average time/residue: 0.1769 time to fit residues: 14.2815 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 : 0.585 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.175159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128822 restraints weight = 5884.479| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.10 r_work: 0.3248 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5814 Z= 0.185 Angle : 0.477 7.148 7930 Z= 0.249 Chirality : 0.037 0.111 868 Planarity : 0.004 0.042 946 Dihedral : 6.794 56.530 742 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.52 % Allowed : 10.74 % 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: 0.09 (0.35), residues: 662 helix: 1.20 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -3.45 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 176 HIS 0.001 0.000 HIS B 246 PHE 0.012 0.001 PHE B 313 TYR 0.014 0.001 TYR A 55 ARG 0.002 0.000 ARG A 95 *********************** 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: 15 poor density : 48 time to evaluate : 0.544 Fit side-chains REVERT: A 88 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: A 95 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.5206 (mpp80) REVERT: A 243 ARG cc_start: 0.7679 (mtp180) cc_final: 0.5940 (mmt180) REVERT: B 88 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: B 95 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.5201 (mpp80) outliers start: 15 outliers final: 8 residues processed: 59 average time/residue: 0.1773 time to fit residues: 14.0044 Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 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 = 0.3892 r_free = 0.3892 target = 0.172631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126815 restraints weight = 6034.358| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.08 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: 0.7459 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5814 Z= 0.198 Angle : 0.481 7.385 7930 Z= 0.252 Chirality : 0.037 0.112 868 Planarity : 0.004 0.044 946 Dihedral : 6.722 58.976 742 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.19 % Allowed : 11.41 % 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: 0.36 (0.35), residues: 662 helix: 1.39 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.24 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.001 0.000 HIS B 164 PHE 0.012 0.001 PHE A 313 TYR 0.015 0.001 TYR B 55 ARG 0.002 0.000 ARG B 95 *********************** 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 66 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.560 Fit side-chains REVERT: A 88 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: A 95 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.5291 (mpp80) REVERT: A 243 ARG cc_start: 0.7703 (mtp180) cc_final: 0.5989 (mmt180) REVERT: B 88 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7642 (m-10) REVERT: B 95 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.5302 (mpp80) outliers start: 19 outliers final: 11 residues processed: 61 average time/residue: 0.1799 time to fit residues: 14.6960 Evaluate side-chains 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 225 CYS 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: 10.0000 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.174453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126913 restraints weight = 6020.455| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.20 r_work: 0.3230 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5814 Z= 0.206 Angle : 0.488 8.114 7930 Z= 0.252 Chirality : 0.037 0.113 868 Planarity : 0.004 0.044 946 Dihedral : 6.679 59.245 742 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.03 % Allowed : 11.74 % Favored : 84.23 % 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: 0.48 (0.35), residues: 662 helix: 1.46 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -3.14 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.001 0.000 HIS A 317 PHE 0.013 0.001 PHE A 313 TYR 0.015 0.001 TYR B 55 ARG 0.002 0.000 ARG B 95 *********************** 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 68 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.589 Fit side-chains REVERT: A 88 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: A 95 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.5287 (mpp80) REVERT: A 172 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6871 (t70) REVERT: A 243 ARG cc_start: 0.7698 (mtp180) cc_final: 0.5918 (mmt180) REVERT: B 88 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: B 95 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.5279 (mpp80) outliers start: 24 outliers final: 13 residues processed: 61 average time/residue: 0.1688 time to fit residues: 14.0820 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 : 0.582 ------------------------------------------------------------------------------- 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 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 214 TRP Chi-restraints excluded: chain B residue 225 CYS 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: 7.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 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 = 0.3919 r_free = 0.3919 target = 0.175601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127557 restraints weight = 6019.434| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.23 r_work: 0.3235 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5814 Z= 0.190 Angle : 0.486 8.564 7930 Z= 0.249 Chirality : 0.037 0.112 868 Planarity : 0.004 0.044 946 Dihedral : 6.539 57.566 742 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.19 % Allowed : 12.92 % 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 (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: 1.57 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.05 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS B 317 PHE 0.012 0.001 PHE A 313 TYR 0.015 0.001 TYR A 55 ARG 0.002 0.000 ARG A 95 *********************** 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 62 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.529 Fit side-chains REVERT: A 88 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: A 95 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.5276 (mpp80) REVERT: A 172 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.7043 (t70) REVERT: A 243 ARG cc_start: 0.7697 (mtp180) cc_final: 0.5921 (mmt180) REVERT: B 88 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: B 95 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.5266 (mpp80) REVERT: B 172 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.7012 (t70) outliers start: 19 outliers final: 11 residues processed: 55 average time/residue: 0.1651 time to fit residues: 12.4978 Evaluate side-chains 59 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 214 TRP Chi-restraints excluded: chain B residue 225 CYS 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: 0.9980 chunk 7 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 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 = 0.3908 r_free = 0.3908 target = 0.174610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126083 restraints weight = 6042.455| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.25 r_work: 0.3211 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5814 Z= 0.225 Angle : 0.507 9.063 7930 Z= 0.259 Chirality : 0.037 0.115 868 Planarity : 0.004 0.045 946 Dihedral : 6.482 55.869 740 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.52 % Allowed : 12.75 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.35), residues: 662 helix: 1.51 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -3.04 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.001 0.000 HIS B 97 PHE 0.013 0.001 PHE A 313 TYR 0.015 0.001 TYR B 55 ARG 0.002 0.000 ARG A 95 *********************** 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 65 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.580 Fit side-chains REVERT: A 88 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7534 (m-10) REVERT: A 95 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5291 (mpp80) REVERT: A 172 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.7025 (t70) REVERT: A 243 ARG cc_start: 0.7696 (mtp180) cc_final: 0.5912 (mmt180) REVERT: B 88 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7617 (m-10) REVERT: B 95 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.5310 (mpp80) REVERT: B 172 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.7039 (t70) outliers start: 21 outliers final: 12 residues processed: 57 average time/residue: 0.1668 time to fit residues: 13.0156 Evaluate side-chains 62 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 214 TRP Chi-restraints excluded: chain B residue 225 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.185091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.139091 restraints weight = 5823.903| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.18 r_work: 0.3252 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5814 Z= 0.164 Angle : 0.484 9.649 7930 Z= 0.244 Chirality : 0.036 0.108 868 Planarity : 0.004 0.044 946 Dihedral : 6.209 53.714 740 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.19 % Allowed : 13.76 % Favored : 83.05 % 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: 0.85 (0.35), residues: 662 helix: 1.72 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -2.98 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS A 309 PHE 0.012 0.001 PHE B 313 TYR 0.016 0.001 TYR B 55 ARG 0.001 0.000 ARG A 95 *********************** 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 58 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.549 Fit side-chains REVERT: A 88 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: A 95 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5398 (mpp80) REVERT: A 172 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.7148 (t70) REVERT: A 243 ARG cc_start: 0.7714 (mtp180) cc_final: 0.5994 (mmt180) REVERT: B 88 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7635 (m-10) REVERT: B 95 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.5422 (mpp80) REVERT: B 172 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.7172 (t70) outliers start: 19 outliers final: 12 residues processed: 53 average time/residue: 0.1667 time to fit residues: 12.1204 Evaluate side-chains 57 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 225 CYS 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: 0.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 33 optimal weight: 0.0000 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.0770 overall best weight: 0.4742 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.182683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135107 restraints weight = 5921.067| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.23 r_work: 0.3265 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5814 Z= 0.147 Angle : 0.475 10.051 7930 Z= 0.237 Chirality : 0.036 0.106 868 Planarity : 0.004 0.043 946 Dihedral : 5.698 49.109 738 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.35 % Allowed : 14.77 % 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: 1.05 (0.36), residues: 662 helix: 1.92 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.01 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 321 HIS 0.001 0.000 HIS A 317 PHE 0.011 0.001 PHE B 313 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG B 95 *********************** 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 57 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.590 Fit side-chains REVERT: A 95 ARG cc_start: 0.6883 (tmm-80) cc_final: 0.5376 (mpp80) REVERT: A 172 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6925 (t70) REVERT: A 243 ARG cc_start: 0.7725 (mtp180) cc_final: 0.5968 (mmt180) REVERT: B 88 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7688 (m-10) REVERT: B 172 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.6991 (t70) outliers start: 14 outliers final: 9 residues processed: 54 average time/residue: 0.1419 time to fit residues: 10.9323 Evaluate side-chains 51 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 88 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 225 CYS 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: 0.0870 chunk 23 optimal weight: 0.3980 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.181150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132946 restraints weight = 5975.443| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.26 r_work: 0.3303 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5814 Z= 0.118 Angle : 0.478 10.381 7930 Z= 0.232 Chirality : 0.035 0.105 868 Planarity : 0.004 0.043 946 Dihedral : 4.536 44.692 728 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.85 % Allowed : 15.77 % Favored : 82.38 % 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: 1.27 (0.36), residues: 662 helix: 2.08 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -2.99 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 321 HIS 0.001 0.000 HIS B 205 PHE 0.011 0.001 PHE B 170 TYR 0.016 0.001 TYR B 55 ARG 0.001 0.000 ARG B 323 ********************** 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 53 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.520 Fit side-chains REVERT: A 88 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: A 95 ARG cc_start: 0.6753 (tmm-80) cc_final: 0.5248 (mpp80) REVERT: A 172 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6535 (t70) REVERT: A 243 ARG cc_start: 0.7704 (mtp180) cc_final: 0.5851 (mmt180) REVERT: B 88 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7560 (m-10) REVERT: B 172 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6617 (t70) REVERT: B 212 GLU cc_start: 0.5232 (tt0) cc_final: 0.5015 (tt0) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.1745 time to fit residues: 12.1351 Evaluate side-chains 50 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 225 CYS 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: 0.7980 chunk 38 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.3234 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.194770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150877 restraints weight = 5768.344| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.11 r_work: 0.3320 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5814 Z= 0.124 Angle : 0.476 10.038 7930 Z= 0.232 Chirality : 0.035 0.104 868 Planarity : 0.004 0.043 946 Dihedral : 4.380 41.298 728 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.34 % Allowed : 16.44 % 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: 1.37 (0.36), residues: 662 helix: 2.13 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -2.94 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 321 HIS 0.001 0.000 HIS A 41 PHE 0.010 0.001 PHE B 170 TYR 0.016 0.001 TYR A 55 ARG 0.005 0.000 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2704.68 seconds wall clock time: 48 minutes 37.60 seconds (2917.60 seconds total)