Starting phenix.real_space_refine on Thu Mar 6 08:40:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4f_44179/03_2025/9b4f_44179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4f_44179/03_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_44179/03_2025/9b4f_44179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4f_44179/03_2025/9b4f_44179.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4f_44179/03_2025/9b4f_44179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4f_44179/03_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-5624/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: 5.24, per 1000 atoms: 0.93 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: 1.37 Conformation dependent library (CDL) restraints added in 571.4 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: 0.45 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: 1.36 Time building geometry restraints manager: 1.61 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: 2.380 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: 17.730 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- 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 : 2.255 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 *********************** 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 : 0.545 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: 0.2130 time to fit residues: 17.2457 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 : 0.536 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.177756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128641 restraints weight = 5825.488| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.21 r_work: 0.3239 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5814 Z= 0.173 Angle : 0.485 6.538 7930 Z= 0.257 Chirality : 0.037 0.120 868 Planarity : 0.004 0.038 946 Dihedral : 7.240 58.563 746 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.52 % Allowed : 8.72 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.34), residues: 662 helix: 0.88 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -3.45 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 176 HIS 0.002 0.000 HIS B 97 PHE 0.013 0.001 PHE B 313 TYR 0.015 0.001 TYR B 55 ARG 0.002 0.000 ARG B 323 *********************** 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 : 0.584 Fit side-chains REVERT: A 88 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: A 95 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5218 (mpp80) REVERT: B 88 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: B 95 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.5158 (mpp80) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 0.1656 time to fit residues: 13.2174 Evaluate side-chains 53 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 0.0670 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.179396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130515 restraints weight = 5892.341| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.22 r_work: 0.3259 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1270 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= 0.151 Angle : 0.456 7.302 7930 Z= 0.238 Chirality : 0.036 0.108 868 Planarity : 0.004 0.041 946 Dihedral : 6.650 57.049 742 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.52 % Allowed : 11.07 % Favored : 86.41 % 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: 0.24 (0.35), residues: 662 helix: 1.31 (0.25), residues: 490 sheet: None (None), residues: 0 loop : -3.38 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.001 0.000 HIS B 317 PHE 0.011 0.001 PHE A 313 TYR 0.015 0.001 TYR B 55 ARG 0.001 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 62 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.567 Fit side-chains REVERT: A 88 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7331 (m-10) REVERT: A 95 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.5150 (mpp80) REVERT: A 243 ARG cc_start: 0.7619 (mtp180) cc_final: 0.5792 (mmt180) REVERT: B 88 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: B 95 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.5151 (mpp80) outliers start: 15 outliers final: 6 residues processed: 56 average time/residue: 0.1965 time to fit residues: 14.8499 Evaluate side-chains 54 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 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 = 0.3919 r_free = 0.3919 target = 0.176142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129217 restraints weight = 5996.918| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.14 r_work: 0.3255 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1371 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= 0.177 Angle : 0.468 7.890 7930 Z= 0.243 Chirality : 0.036 0.109 868 Planarity : 0.004 0.042 946 Dihedral : 6.575 58.989 742 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.19 % Allowed : 11.07 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.35), residues: 662 helix: 1.50 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -3.16 (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 B 317 PHE 0.012 0.001 PHE A 313 TYR 0.014 0.001 TYR A 55 ARG 0.001 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 67 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.572 Fit side-chains REVERT: A 88 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7515 (m-10) REVERT: A 95 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.5217 (mpp80) REVERT: A 172 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.7001 (t70) REVERT: A 243 ARG cc_start: 0.7690 (mtp180) cc_final: 0.5940 (mmt180) REVERT: B 88 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7608 (m-10) REVERT: B 95 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.5209 (mpp80) REVERT: B 172 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6991 (t70) outliers start: 19 outliers final: 10 residues processed: 61 average time/residue: 0.1771 time to fit residues: 14.6356 Evaluate side-chains 59 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.179206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131501 restraints weight = 5936.684| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.19 r_work: 0.3237 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1451 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 8.301 7930 Z= 0.251 Chirality : 0.037 0.113 868 Planarity : 0.004 0.043 946 Dihedral : 6.586 58.963 742 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.69 % Allowed : 12.42 % 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: 0.70 (0.35), residues: 662 helix: 1.69 (0.25), residues: 476 sheet: None (None), residues: 0 loop : -2.97 (0.46), residues: 186 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 0.012 0.001 PHE B 313 TYR 0.015 0.001 TYR A 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 65 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.581 Fit side-chains REVERT: A 88 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: A 95 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.5266 (mpp80) REVERT: A 172 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.7187 (t70) REVERT: A 243 ARG cc_start: 0.7714 (mtp180) cc_final: 0.5989 (mmt180) REVERT: B 88 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7653 (m-10) REVERT: B 95 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.5277 (mpp80) REVERT: B 172 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.7166 (t70) outliers start: 22 outliers final: 8 residues processed: 58 average time/residue: 0.1669 time to fit residues: 13.2428 Evaluate side-chains 55 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 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 = 0.4029 r_free = 0.4029 target = 0.184370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138049 restraints weight = 5872.627| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.19 r_work: 0.3243 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1601 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= 0.186 Angle : 0.482 8.758 7930 Z= 0.246 Chirality : 0.037 0.110 868 Planarity : 0.004 0.043 946 Dihedral : 6.446 57.075 742 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.85 % Allowed : 13.59 % Favored : 83.56 % 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: 0.84 (0.35), residues: 662 helix: 1.80 (0.25), residues: 476 sheet: None (None), residues: 0 loop : -2.93 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.001 0.000 HIS B 317 PHE 0.012 0.001 PHE B 313 TYR 0.015 0.001 TYR A 55 ARG 0.001 0.000 ARG B 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 60 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.607 Fit side-chains REVERT: A 88 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: A 95 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.5282 (mpp80) REVERT: A 172 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.7149 (t70) REVERT: A 243 ARG cc_start: 0.7703 (mtp180) cc_final: 0.5967 (mmt180) REVERT: B 88 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: B 95 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.5346 (mpp80) REVERT: B 172 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.7129 (t70) outliers start: 17 outliers final: 7 residues processed: 53 average time/residue: 0.1700 time to fit residues: 12.3850 Evaluate side-chains 55 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 7 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 60 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.183488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136028 restraints weight = 5931.084| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.22 r_work: 0.3259 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1717 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= 0.159 Angle : 0.474 9.212 7930 Z= 0.239 Chirality : 0.036 0.107 868 Planarity : 0.004 0.043 946 Dihedral : 6.017 53.870 738 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.52 % Allowed : 14.60 % 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: 1.75 (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 317 PHE 0.011 0.001 PHE A 313 TYR 0.015 0.001 TYR B 55 ARG 0.001 0.000 ARG B 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 58 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.606 Fit side-chains REVERT: A 88 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: A 95 ARG cc_start: 0.6907 (tmm-80) cc_final: 0.5369 (mpp80) REVERT: A 172 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6970 (t70) REVERT: A 243 ARG cc_start: 0.7681 (mtp180) cc_final: 0.5905 (mmt180) REVERT: B 88 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: B 172 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6973 (t70) outliers start: 15 outliers final: 9 residues processed: 52 average time/residue: 0.1548 time to fit residues: 11.4173 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 : 0.519 ------------------------------------------------------------------------------- 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 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 172 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 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 = 0.3971 r_free = 0.3971 target = 0.181106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133377 restraints weight = 5859.520| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.20 r_work: 0.3253 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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= 0.175 Angle : 0.495 9.736 7930 Z= 0.245 Chirality : 0.036 0.109 868 Planarity : 0.004 0.043 946 Dihedral : 5.297 52.051 730 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.85 % Allowed : 14.60 % 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: 0.91 (0.35), residues: 662 helix: 1.81 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.06 (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 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 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.535 Fit side-chains REVERT: A 88 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7364 (m-10) REVERT: A 95 ARG cc_start: 0.6869 (tmm-80) cc_final: 0.5273 (mpp80) REVERT: A 172 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6985 (t70) REVERT: A 243 ARG cc_start: 0.7715 (mtp180) cc_final: 0.5913 (mmt180) REVERT: B 88 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7570 (m-10) REVERT: B 172 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6985 (t70) outliers start: 17 outliers final: 13 residues processed: 52 average time/residue: 0.1483 time to fit residues: 10.9646 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 : 0.529 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.181378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133774 restraints weight = 5882.232| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.20 r_work: 0.3270 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1821 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= 0.166 Angle : 0.492 10.044 7930 Z= 0.243 Chirality : 0.036 0.109 868 Planarity : 0.004 0.043 946 Dihedral : 5.156 48.762 730 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.85 % Allowed : 14.77 % 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: 0.98 (0.35), residues: 662 helix: 1.86 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.04 (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 A 313 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG A 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 56 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.529 Fit side-chains REVERT: A 88 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: A 95 ARG cc_start: 0.6835 (tmm-80) cc_final: 0.5240 (mpp80) REVERT: A 172 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6969 (t70) REVERT: A 243 ARG cc_start: 0.7744 (mtp180) cc_final: 0.5992 (mmt180) REVERT: B 88 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: B 172 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.6964 (t70) outliers start: 17 outliers final: 13 residues processed: 52 average time/residue: 0.1494 time to fit residues: 11.0731 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 : 0.558 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.177824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129730 restraints weight = 6019.204| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.21 r_work: 0.3242 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1821 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= 0.189 Angle : 0.508 10.292 7930 Z= 0.250 Chirality : 0.037 0.111 868 Planarity : 0.004 0.044 946 Dihedral : 5.100 47.052 730 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.68 % Allowed : 15.10 % 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: 0.94 (0.35), residues: 662 helix: 1.83 (0.25), residues: 486 sheet: None (None), residues: 0 loop : -3.04 (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 0.012 0.001 PHE B 313 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG A 95 ********************** 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 55 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.544 Fit side-chains REVERT: A 88 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7568 (m-10) REVERT: A 95 ARG cc_start: 0.6886 (tmm-80) cc_final: 0.5301 (mpp80) REVERT: A 172 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.7005 (t70) REVERT: A 243 ARG cc_start: 0.7756 (mtp180) cc_final: 0.6018 (mmt180) REVERT: B 88 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7646 (m-10) REVERT: B 172 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.7013 (t70) outliers start: 16 outliers final: 12 residues processed: 51 average time/residue: 0.1600 time to fit residues: 11.4867 Evaluate side-chains 55 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.0040 chunk 50 optimal weight: 0.0030 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 0.4602 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.178304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130980 restraints weight = 5916.247| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.18 r_work: 0.3269 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1915 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= 0.143 Angle : 0.486 10.231 7930 Z= 0.238 Chirality : 0.036 0.107 868 Planarity : 0.004 0.043 946 Dihedral : 4.901 43.770 730 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.57 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: 1.13 (0.36), residues: 662 helix: 1.95 (0.25), residues: 488 sheet: None (None), residues: 0 loop : -2.96 (0.47), 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 317 PHE 0.010 0.001 PHE B 313 TYR 0.016 0.001 TYR A 55 ARG 0.001 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.85 seconds wall clock time: 47 minutes 23.01 seconds (2843.01 seconds total)